Ok, checking back, I see now... X5. Was talking about Z4 instead, my bad.
In regards to his X5 "death." Not unless you count X has having died as well. Everyone assumes his survival because X too survived. The fact that X didn't find anything but the Z-saber was all the more reason for Zero to be alive. X never had any doubts and even feels his presence at times. Nobody but Gate really assumes he has died, and even if he actually did, he was revived again. As a matter of fact, if Zero himself is to be literally believed; he never died, not even in X1.
Whereas in regards to Z4, him being missing is directly related to never being seen again, therefore he's dead from that point onward.