It sounds a bit like by "are they group isomorphisms" you are really asking "are they only group isomorphisms and not ring isomorphisms?" Of course they are additive group isomorphisms, but they are actually more than that.
While the individual Hom groups aren't rings, the sum $\bigoplus_{1\leq i,j\leq k}\text{Hom}_R\left(M_i^{n_i},M_j^{n_j}\right)$ is a ring!
Perhaps the way to get comfortable with it is to imagine it as a "formal" ring of matrices with entries from the Hom groups. Then formal matrix multiplication composes them in a reasonable way such it is a ring. The matrix multiplication matches the composition in $\mathrm{End}_R(M)$ exactly through the map, so it is a ring homomorphism. This holds even if the $M_i$ lack their special properties (being pairwise nonisomorphic simple modules.)
In the passage from line (1) to (2), we simply eliminate a lot of superfluous terms in the direct sum and discover that the multiplication boils down to coordinatewise multiplication of a direct product of rings. That is what the pairwise nonisomorphic condition buys us.
So, the isomorphisms involved are ring isomorphism all the way through.
Here's another sort of example. Let $e$ be an idempotent in any ring with identity, and let $f=1-e$. Then one can show that $R\cong \begin{bmatrix}eRe&eRf\\fRe&fRf\end{bmatrix}$ as rings, where the multiplication on the right is formal matrix multiplication. Neither $eRf$ nor $fRe$ has to be a ring, but $eRe$ and $fRf$ are both rings.
You can look upon this as $R\cong\mathrm{End}_R(R)\cong \mathrm{End}_R(eR\oplus fR)=\mathrm{Hom}_R(eR\oplus fR,eR\oplus fR)\cong\begin{bmatrix}\mathrm{Hom}_R(eR,eR)&\mathrm{Hom}_R(fR,eR)\\\mathrm{Hom}_R(eR,fR)&\mathrm{Hom}_R(fR,fR)\end{bmatrix}$
The (group) isomorphism $\mathrm{Hom}_R(fR,eR)\cong eRf$ can be found in Lam's First course in noncommutative rings (Proposition 21.6.) It turns out to be a ring isomorphism if $e=f$.
Since you confirmed it in the comment above:
It sounds like the intended context was an algebraically closed field, and that $H^\ast$ is a commutative semisimple ring.
Using the Artin-wedderburn theorem it is easy to see why all the matrices must have side length $1$ in order to be commutative. That makes a product of fields, each one a finite field extension of $k$. But adding algebraiclly closed means that these fields are in fact just $k$.
Best Answer
A finite product of fields is clearly Artinian.
It's also then clearly Jacobson semisimple (since it has no nonzero nilpotent elements, and the radical is nilpotent.)
Since Jacobson radical zero and Artinian combine to make "semisimple," we're done.