I keep having this problem and it has nothing to do with being homeless, as far as I can tell... For example, the most recent occurence was today when I loaded up my game after updating it to the most current version, and I go to play one of my families (I'm rotating through a few related families) and the wife is missing. Just gone from the family. She was an adult, one of the neighborhood-created "Crumps" originally but she married into my Sim family and they had 3 kids so far. She's not even in their relationship panel anymore, so she didn't just die. She's just totally gone as if she never existed.
Oddly enough, this wasn't long after she had twins (with no fertility treatment) that seemed to have inherited none of her genetics - she's black with black hair, and her husband is dark-skinned with black hair, and these twins came out white as white can be with blonde hair. So I'm not sure if it's related or not but I thought it was weird.
This has happened several times where I load the game the next day and a Sim I was playing disappeared from the household and entire game, without having had died. Very frustrating. I have no custom content, keep my game updated, etc.