Couldn't the original bit about the weapons, and even armor, be compared to Classic Mega Man, Metriod, Battle Network, Star Force, and Legends?
My guess is that the programmers were lazy and made a forced deletion, leaving it to be a mystery. My actual guess is that (and it ONLY applies to Classic and X) the weapon data erases itself after a certain period of time. As for why the hell Trigger doesn't have the same damn weapons as before, though, doesn't make a lick of sense.
For the armor, X could just have put it in some kind of 'hall of fame'. The Ultimate Armor is a bigger question, because the only non-code time I think you can get it is in X5, which makes sense, but it's also possible to get it at the start of the game, and even in X4 it's available.