Yes and federation works. The caveat is that since Matrix s2s de facto mandates TLS certs, you'll need to use self-signed certs as well as accept them from other onion peers. I've been aware of some more involved setups where a server name on the clearnet can be manually mapped to its Tor onionsite as well.

Beyond that, c2s is just a simple HTTP service, and most clients should support it assuming they have a way to hop on Tor (Orbot, SOCKS5 proxy etc)