I expect that federated onion homeservers, forming a "dark Matrix", will work but that there will be issues with federating onion and clearnet homeservers. This isn't unusual, and the same applies to fediverse instances.
Running on onion addresses does provide some security advantages, but also it means that you don't need to buy a clearnet domain, you don't need to forward any ports and so could be behind a hostile internet router and you don't need to care about obtaining TLS certificates. There was a talk on the first day of 35C3 about TLS1.3 which also described the many issues with TLS and what a dumpster fire it is. In a lot of ways using onion addresses is more convenient and with better security properties, so long as you don't mind the long random strings or QR codes.