Let $G_1=(V_1,E_1)$ and $G_2=(V_2, E_2)$ be two isomorphic graphs.
If $V_1= \{ v_1,.., v_n\}$ and $V_2=\{w_1,..,w_n\}$ and $f: V_1 \to V_2$ is the isomorphism, you can define a permutation $\sigma$ via
$$f(v_i)=w_{\sigma(i)}$$
Now, if $P:=P_\sigma$ is the corresponding permutation matrix, then you have
$$A_1=PA_2 P^{-1}$$
from where you can deduce that $A_1,A_2$ have the same spectrum.
You can do something here, but it's not great.
For the isomorphism, we describe a bijection between $V(G)$ and $V(H)$ by its permutation matrix. For the homomorphism, we have a function $f \colon V(G) \to V(H)$, which we can also describe by a matrix $F$ such that $F_{ij} = 1$ if $f$ maps the $i^{\text{th}}$ vertex of $A$ to the $j^{\text{th}}$ vertex of $B$. I will assume $V(G) = \{1,\dots,n\}$ and $V(H) = \{1,\dots,m\}$ just so we can say $F_{ij}=1 \iff f(i)=j$. Note that $F$ is not even square; in general, it is an $n \times m$ matrix.
If $A(G)$ and $A(H)$ are the adjacency matrices of $G$ and $H$, then $F A(H) F^{\mathsf T}$ is the matrix whose $(i,j)$-th entry is the sum of all products of the form $F_{ik} A(H)_{kl} F_{jl}$. We have $F_{ik}=1$ only if $k = f(i)$, and $F_{jl}=1$ only if $l = f(j)$, so actually $F A(H) F^{\mathsf T}$ is the matrix whose $(i,j)$-th entry is equal to $1$ if and only if $f(i)$ is adjacent to $f(j)$.
For the function $f$ to be a homomorphism, we want $f(i)$ to be adjacent to $f(j)$ whenever $i$ is adjacent to $j$. This is described by the adjacency matrix inequality $$A(G) \le F A(H) F^{\mathsf T}.$$ By this, I mean that every entry of $A(G)$ is less than or equal to the corresponding entry of $F A(H) F^{\mathsf T}$.
Best Answer
Assumption. $0 \leq n \leq m < N$ are integers.
Let's start with a simple version of your problem in which we drop the requirement of undirectedness.
Let $g(i) \equiv {}_{N-1} C_i \cdot {}_2F_1(1, i - N + 1; i + 1; -1)$ where ${}_a C_b$ is the binomial coefficient and ${}_2F_1{}$ is the ordinary hypergeometric function.
Lemma (Counting digraphs). There are exactly $(g(n) - g(m+1))^N$ directed graphs with (i) $N$ nodes, (ii) $n \leq \operatorname{outdeg}(v) \leq m$, and (iii) no self-loops (i.e., no edges of the form $v \rightarrow v$).
By symmetry, the above also holds if we replace $\operatorname{outdeg}$ with $\operatorname{indeg}$.
Proof. There are ${}_{N-1} C_k$ ways to assign $k$ edges to a single node if we exclude self-loops. It follows that there are $\sum_{k = n}^m {}_{N-1} C_k = \sum_{k = 0}^m {}_{N-1} C_k - \sum_{k = 0}^{n-1} {}_{N-1} C_k$ ways to assign edges to a single node. Some tedious algebra reveals that $\sum_{k = 0}^{\ell-1} {}_{N-1} C_k = 2^{N-1} - g(\ell)$, from which the result follows.
Figure. $\log$ of the number of digraphs when $n = 0$ (values $m \geq N$ are capped to $N - 1$).
Let's return to your original problem. This problem is much harder because unlike the simpler problem above, one cannot "uncouple" the nodes of the graph to obtain an expression of the form $(\cdot)^N$.
Let $\mathbb{N}$ denote the nonnegative integers. When $k$ is a positive integer, let $\mathbb{N}^k$ denote the usual Cartesian product. For convenience, let $A^0 \equiv \{ 0 \}$ for any set $A$. Let $\mathbf{x}_{(-1)} \equiv (x_2, \ldots, x_N)$ denote the vector $\mathbf{x}$ with its first co-ordinate removed. When $\mathbf{x} \equiv (x_1)$ is a singleton vector, we interpret this as $\mathbf{x}_{(-1)} \equiv 0$.
Let $u_0(0) = 1$. For each positive integer $k \leq N$, let $u_k : \mathbb{N}^k \rightarrow \mathbb{N}$ by $$ u_k(\mathbf{x}) = \sum_{\mathbf{y} \in \mathcal{Y}} u_{k-1}(\mathbf{x}_{(-1)} + \mathbf{y}) \qquad \text{where} \qquad \mathcal{Y} \equiv \left \{ \mathbf{y} \in \{0,1\}^{k-1} \colon n \leq x_1 + \mathbf{1} \cdot \mathbf{y} \leq m \right \}. $$
Lemma (Counting undirected graphs). There are exactly $u_N(\mathbf{0})$ undirected graphs satisfying the same properties (i), (ii), and (iii) as above.
Code implementing the recurrence is given at the end of this post. Note, however, that this code only has a slight edge over the naive $O(2^{N^2})$ algorithm involving enumerating all possibilities.
Figure. $\log$ of the number of undirected graphs when $n = 0$.