what do you mean by Canon? sorry im not that geeky yet... the radiation fallout is still drifting my way on all the nerd language stuff.
Canon, or you could also say Fallout lore = A official integrated part of the Fallout universe and with that tied to its plotlines timeline aswell as future content etc.
The Brotherhood of Steel for instance is canon, Vault 0 from Fallout Tactics is not canon which means it is treated as "never existed in future Fallout games.
The aliens were so far only part of eastereggs in Fallout 1 and Fallout 2 but not really part of the canon. Just funny things hidden as randon encounters in the games to make players laugh but they did not really exist or had any significance in the overall Fallout universe.
Maybe Bethesda decided to change that now, dont know , maybe they will say something to that in a future interview but the majority of Fallout fans would not like that at all and propably not accept it. I wouldn't. I like the aliens as part of a ongoing Fallout franchise running gag but thats it.
So i really hope that they make Mothership Zeta a funny easteregg DLC with a non-canon plot on its own without any connection to the rest of the Fallout world or the fans will pull the emergeny brake and reject to accept it as canon to save Fallout from total trash pop culturification. (Does such a word exist ?) LOL