You cannot construct what is not there.
When we construct the real numbers from the rational numbers, we don't invent them out of thin air. We use material around us: sets of rational numbers (or sets of functions which are sets of sets of rational numbers). And similarly when we want to construct a dual vector space, we don't wave our hands and whisper some ancient texts from the Necronomicon ex Mortis. We use the sets at our disposal (and the assumptions they satisfy certain properties) to show we can define a structure with the wanted properties.
So the real numbers, and dual vector spaces, and all the other mathematical constructions, have existed in your fixed universe of sets before you began your work. What we do, if so, is not as much as constructing as we are defining them and using our axioms to argue that as the definition "makes sense" (whatever that means in the relevant context), such objects exist.
"Okay, Asaf, but what does all that have to do with my question?", you might be asking yourself, or me, at this point. Well, if you don't interrupt me, I might as well tell you.
The von Neumann universe is a way to represent a universe of $\sf ZF$ as constructed from below. But it is using the pre-existing sets of the universe. What is clever in this construction is that it exhaust all the sets of the universe. And if the universe only satisfied $\sf ZF-Reg$, then the result is the largest transitive class which will satisfy $\sf ZF$.
But what happens in different models of set theory? Well, we can prove from $\sf ZF$ that the von Neumann hierarchy, which has a relatively simple definition in the language of set theory, exhausts the universe. So each different model will have a different von Neumann hierarchy. And models which are not well-founded, will have a non-well-founded von Neumann hierarchy.
So yes, we first need a model of $\sf ZF$ in order to construct this hierarchy, but we don't need it inside the theory. We need it in the meta-theory. Namely, if you are working with $\sf ZF$, then you most likely assume it is consistent in your meta-theory, where you formalize your arguments and do things like induction on formulas. And that is enough to prove the existence of the von Neumann hierarchy; because once you work inside $\sf ZF$, the whole universe is given to you!
I'll take a swing at answering the question that I think you are trying to ask. I'll formulate it as follows:
If foundations are important as the name suggests and the so-called
"foundational crisis" suggests, why do so few mathematicians concern
themselves much with them nowadays. If foundations aren't important,
then why was there a "foundational crisis" and a significant effort to
create foundations?
tl;dr "Foundations" and ZFC were created to solve a fairly specific problem (founding real analysis), which they did. Now we don't worry about the problem, so many mathematicians don't have much reason to "faff about" with foundations.
The first thing to note is the obvious statement that mathematics has been done before, during, and after the establishment of ZFC as a foundational system. Just as clearly, very little mathematics prior to the establishment of ZFC has been deemed "incorrect" since its establishment. (Even the parts that arguably may have been have often been "revitalized" in modern treatments, sometimes utilizing other foundational approaches, e.g. "infinitesimals".)
So the first point is "doing math" doesn't require a foundational system as witnessed by the fact that math was being done for thousands of years before the advent of ZFC or anything like it. This is also witnessed by the fact that you can learn quite a bit of math today without concerning yourself much with the details of ZFC.
My understanding of the situation near the "foundational crisis", which may well be wrong - I'm no math historian - is there was a fairly specific group that wanted something like set theory: real analysts (as we'd call them nowadays). My reading of the situation is that it was the controversies and vagaries in real analysis that sparked mathematical (as opposed to philosophical) interest in foundations. Intuitions about "real numbers", "functions", "continuous functions" were not enough for the mathematicians of the day to converge on questions like what the Fourier transform of the constant function should be or whether it should even exist. This also raised the possibility that the notion of "real numbers" itself might be incoherent.
This led to the early work on defining the reals and defining a notion of function. (There were also philosophical motivations for this work that were likely partially independent, but I suspect that without the issues in real analysis mathematicians would have largely ignored such work.) Of course, from there Russell's paradox scuttled the still largely intuitive conception of naive set theory. This likely also scuttled the idea that we could rely on mathematical intuition alone and reinforced the possibility that, e.g., the real numbers really could be built on quicksand. They certainly were in naive set theories. Then we had 40 years of many proposed foundational systems, modifications to those systems, critiques of those systems, meta-logical analyses of those systems, and hands-on work using the systems. Presumably the majority of mathematicians of the time were at most spectators to this. They continued to plod on doing math the way they'd always done it likely without much concern if they were, say, a (non-analytic) number theorist.
I would say the main go/no-go issue for a set theory of that time would be whether it could found real analysis, i.e. construct the real numbers, construct a notion of continuous function, and prove widely accepted results like Heine-Borel. Jumping to the modern day, yes, it is the case that the mere existence of any acceptable foundation removes much of the urgency of the "foundational crisis". Most mathematicians during the "foundational crisis" didn't care about sets, they cared about real numbers and continuous functions. Given some other (non-set-theoretic) framework to assuage their concerns, they would have had little interest in set theory. Nowadays, students (perhaps unfortunately...) don't have these concerns in the first place, so they have little reason to devote much or any time to foundations. Set theory is usually taught in a naive way with some warnings. The language and tools from set theory are useful even without it being a foundational system, so it's not ignored entirely.
The variety of foundational systems, the fact most of them are also capable of serving as a foundation for real analysis and most other branches of math, and the fact that ZFC itself goes far beyond what is needed by most mathematicians means most of mathematics doesn't really depend on the specific details of the underlying foundational system. For example, while finding an inconsistency in ZFC would be big news, it's hard to imagine that it would also impact all other foundational systems that are capable of supporting e.g. real analysis. It is likely that most results would be unaffected and the ones that were affected would be relatively easily adapted and still "morally true". Maybe an extra assumption is added, say.
Another aspect of this is that there are many results in more solidly grounded fields like number theory that have proofs that use mathematical objects in less solidly grounded fields like real analysis. To the extent these results have "elementary" proofs within the more solidly grounded field, we have a web of justification for the validity of non-trivial aspects of the less solidly grounded field. This puts some limits on how "wrong" we could be in those fields before we'd have to be "wrong about everything".
Best Answer
It is true that, if $\mathsf{ZFC}$ is consistent, $\mathsf{CH}$ is undecidable within it. This is just one example of a more general fact: any consistent recursively enumerable first-order theory at least as strong as Peano arithmetic contains a statement undecidable in that theory. This is the first of Gödel's incompleteness theorems; the second gives an example, namely a statement calling the theory consistent.
The real question isn't whether $\mathsf{ZFC}$ has known limitations of this kind; of course it does. The question is which other statements we should add as axioms. The $\mathsf{C}$ in $\mathsf{ZFC}$ is the axiom of choice, which is itself undecidable in $\mathsf{ZF}$. The history of set theory has seen much broader support in favour of adding $\mathsf{AC}$ than in favour of subsequently adding $\mathsf{CH}$.
Why? Well, let's look at some of the differences: