I've never quite known what the cause is, but I've been killed while wandering around my ship since they made the changes. My guess is that it might be based on whether the structure you are inside is considered to be fully enclosed or not. So, if you go inside a room and close a plex-door, you might be fully enclosed. If you go inside a room and close a rail-door, you might be considered to still be in open space. Thus, while I'm walking around on the bridge or corridors of my ship, the fact that the airlocks on my ship are rail-doors means, ironically, that I'm exposed to space.
[doublepost=1479142924,1479142400][/doublepost]I've been playing single-player and just doing ship building while waiting for the faction changes to come out. On occasion I've been attacked by pirates. My ship-building sector, being full of ships, isn't concerned with the appearance of an Isanth or two, so I don't pay much attention to them (I'm more worried about friendly fire.) As such, I've quit out while my ships were firing at long range targets that were proving difficult for the Bobby AI turrets to hit. When I reloaded the saved game, my recollection is that the pirates were no longer present. My assumption has been that the saved file doesn't track the position of random spawns.
The same is also true of overheated ships that are on countdown. I've quit the game while such derelicts still had plenty of time on their countdown, and found them gone when I restart the game.