I believe that you may have misstated the definition of what it means to be an $\in$-homomorphism. (I couldn't find your notion in Jech at your links — have I missed it?)
For example, with your definition, $f(X)$ is always a set, and never an atom, and so if there are atoms, then the identity function will not be a $\in$-homomorphism. Your definition seems to require us to map all atoms to $\emptyset$. Further, your notion would require $f$ to fix all well-founded sets, since there could be no $\in$-minimal set that is moved. In ZFC, therefore, your notion trivializes. Your definition also seems to presume that the models are transitive, using the standard $\in$-relation, whereas the notion of homomorphism should be sensible with arbitrary models of set theory.
I believe that the intended notion of homomorphism should be the one obtained by viewing models of set theory as relational structures $\langle M,\in^M\rangle$, a domain $M$ with a binary relation $\in^M$. In this case, the standard model-theoretic notion of (strong) $\in$-homomorphism or $\in$-embedding between two such structures would be a map $j:M\to N$ such that
$$x\in^M y\iff j(x)\in^N j(y)$$
for all $x,y\in M$.
The difference between this and your notion is that you require that $j(y)$ has no other $\in^N$ elements except the $j(x)$ objects.
I analyzed this homomorphism notion in my paper
One of the main results was that the countable models of set theory are linearly pre-ordered by embedding:
Theorem. For any two countable models of set theory $\langle M,\in^M\rangle$, $\langle N,\in^N\rangle$, one of them is isomorphic to a submodel of the other.
This notion of submodel is the model-theoretic notion of $\in$-homomorphism, which are necessarily injective and thus isomorphisms of the domain with the range.
The theorem is often found surprising, but this is mainly because this notion of submodel is much weaker than we usually consider in set theory. In particular, submodels in this sense need not preserve much set-theoretic truth; they need not even be $\Delta_0$-elementary. This is a reason to view $\in$-homomorphisms as much weaker than we probably want. Set theorists typically want to consider emeddings that are at least $\Delta_0$-elementary, preserving $\Delta_0$ truth.
To illustrate the difference, the map $j:V\to V$ defined by
$$j(y)=\{j(x)\mid x\in y\}\cup\{\{\emptyset,y\}\}$$
has $x\in y\iff j(x)\in j(y)$, and it is therefore an $\in$-embedding of $V$ into $V$. And yet, it has no fixed points — it does not even fix the natural numbers to themselves, and it does not carry $\emptyset$ to $\emptyset$.
Another part of my answer to your question is to mention my paper (updated from my initial post, which had mentioned the wrong paper):
In that paper, we considered for various anti-foundational theories whether there can be nontrivial elementary embeddings $j:V\to V$. Some of the arguments involve Quine atoms in the anti-foundational theories, but these function essentially similarly to urelements in ZFA, and the relevant notion of embedding is your notion of $\in$-homomorphism. I'd encourage you to take a look there.