@crinrict Thanks for looking into it/adding it.
Just some new info, which may or may not help. (I could/should have added this before, just didn't find the time to do it.)
By now we have figured out that the 'guilty criminal' hidden trait is removed once a Sim is no longer a suspect. From what you've said it means that these Sims should be removed after that. Which, for some reason, doesn't happen and turns them into steath Sims. I'm not sure it's just criminals that do it, I do remember players other than myself mentioning doctors, but they could be ex-cons of course 😉.
As for the parallel with pregnant Sims, I can tell you that in my game they are not removed after giving birth. They are, however, visible in manage households. The two that I have treated both were in a four person household, with, presumably, their husband, teenage daughter and child son. But neither of them had a baby - yet it is possible for NPCs to have babies in their households. I have seen it before in a different save, it could of course be patched out later, but not that I've heard/read. (not sure if this is relevant, or a different issue, but I thought I'd mention it, just in case it's connected)
I'm going to bump my forum thread to find out if anyone has new insights. I'll edit this message should anyone find out anything interesting.
EDIT: HarmonySims280 has let me know that apparently the MC Command Center mod from Mod the Sims has a fix for 'stealth' Sims. I'm assuming this will be helpful to fix it in game (so that it also works properly for people that don't use mods).
The post from Harmony: http://forums.thesims.com/en_US/discussion/comment/13692183#Comment_13692183
The MTS link: http://www.modthesims.info/download.php?t=551680
