(Further Matrix Online spoilers) The main storyline of the bulk of the time that The Matrix Online was, uh, online was the resurrection of Neo (or "the retrieval of Neo from the Source" if you prefer that nomenclature). Morpheus sacrificed himself as a part of that effort.

From the stand point of "Morpheus sacrificed himself for Neo", that's a good story, even if very few players were around for the game event where that happened "on screen". I think its a pretty decent excuse for "Morpheus isn't involved in Matrix 4" even if I do hope that they find a way somehow to tell that story in a better way than "well if you look for the right YouTuber you might get an okay retelling of what playing The Matrix Online was like" and/or compilations of the live events cutscenes. (Related aside: Owning what was once the developer Monolith, Warnermedia should own all of the assets of The Matrix Online, except maybe remaining clauses in publishing contracts with Sega/Sony/what is today Daybreak. I wonder if some sort of F2P revival might have been an interesting marketing plan for Matrix 4.)

I don't have any direct theories on Trinity's return. There's rumors about where Matrix Online's storyline was supposed to go before the game was shutdown, of course, but rumors of a storyline and events that didn't even happen are certainly non-canon. I am of course very curious to see how they address it.

They're probably digital backups of uploaded memories or something like that. Both of their bodies were at the Machine City at the end of the trilogy, after all.