No legitimate reason for that, I'm just bored. Most of them (if not all) disappear after their roles in their missions are over, please remind me who doesn't so I can blow up their station/ship and collect those people as trophies.
For example, the dude who flew the Xperimental shuttle bailed, got picked up by me and later ejected in paranid prime now permanently takes up a docking bay in paranid shipyard. A moment ago I blew up the goner temple and picked up an astronaut called "goner database".
A bit of side notes though, people said if we keep killing xenon in a xenon sector after 2 in-game days their respawn will slow down. However, I've been homebased in 347 for more than 3 in-game days, with non-stop patrols of several destroyers, destroyed the xenon station several times but they keep coming. I just want to know if it's possible at all to "slow down the respawns to once per 24 hrs", if not I'll just pull back and leave half the sector to roaming xenons. Right now my patrols are aggressively hunting down every xenon ships in the sector.