Since Zero Mission references Prime, it's canonical. Since the Prime games are canonical, and Corruption references Hunters, it's also canonical (sigh).
Oh, I'm not debating whether Prime is canonical. I know it is. In fact, I've already stated this. I'm only pointing out how loose the canon is. Same with Zelda.
As for your logic about SM not mentioning Prime, then most prequels shouldn't count since they are usually not mentioned. The Prime games majorly reference the other games in the series. You are free to think what you want, I just hope you remember that all of the Metroid games are canon (including the Fusion is the last).
I kind of feel like Samus would have mentioned when radioactive goo corrupted her body and almost killed her..... Just saying....
OOT didn't retcon anything, everything in the games before and after are still canon (retcon means it changes established canon).
Are you kidding me? ALL of the maidens, descendants of the sages (2 of which are a fish girl and a rock beast), in A Link to the Past are regular human/Hylian girls. The Zoras are still alive and well too (no evolutionary Zora descended Rito tribe here either), except they aren't humanoid bipedal fish creatures, they're green and orange fish monsters. Seriously, dude.....
brood, screw Sakamoto. He should not have been allowed to direct a Metroid game again. Luckily he has zero say over what is or isn't canon in Metroid.
What is this? I don't even.....
So the man who co-created the series and has directed every main series entry starting with Metroid II has no say in what is series canon? I just....
/facepalm