Yes absolutely. Not only are they federated, but they are even exposed via the API, as described in more detail at https://piefed.social/c/piefed_api/p/1596518/emoji-reactions-in-the-piefed-api. Of course it is up to each third-party app to decide how or whether to do anything with that, but it’s there whenever they are ready for it, and emojis show on the PieFed web UI.

See also https://codeberg.org/fediverse/fep/src/branch/main/fep/9098/fep-9098.md e.g.:

This document is based on implementations of custom emojis in Pleroma, Mastodon, Misskey and Fedibird.

That said, I am not certain if they can all interrelate currently, as opposed to merely representing similar ideals. This should help get you started if you wanted to do more deep diving though:-).