As has been pointed out a little, structures don't house sims, they have collections of 'buckets'. The entire engine works on the basis of representing everything as resource tokens and resource buckets. Sims only exist in 'agent' form when going from one bucket to the next, at which point they increase the relevant bucket count and cease to exist.
You can see a lot of the buckets and their values on the data maps. Even things like tech level and education are represented using tokens and buckets. Think of everything like the power and water services, but instead of sending out power tokens along the roads to fill up power buckets, you could have houses sending out kid tokens to fill up the school's kid bucket. At the end of class, the school sends out kid tokens, with a tacked on education token, that fills up the kid and education buckets of houses.
(As a side note, if you destroy a bunch of houses while kids are in class, the 'excess' kid agents go to a school bus stop and vanish when they can't find a free kid bucket. Same with workers, only they 'leave town' if in a car).
Now, what if this 'phantom' population is another bucket? The size of the bucket increases and descreases based on the number of houses you have, and tokens are added to it when houses are added (so basically if it never 'spends' tokens it will always be full).
Let's call it a reserve bucket. What happens if a bunch of agents 'die'? or resource buckets containing worker/shopper/kid tokens get deleted without being able to generate those potential agents (demolish, disaster, disconnected then demolished roads, untreated injuries, etc)? You end up with partially filled worker/shopper/student buckets. Kill enough tokens and you just have a ghost town.
Maybe the reserve bucket spends it's tokens to refill the empty ones? And perhaps it refills gradually over time so, provided you don't go on a token slaughtering rampage, you will always have a functioning simulation. The larger your city, the larger the reserve and the more tolerant to a meteor bullseyeing your high school.
Maybe it's not part of the visual simulation, but it would still function within it. Pretend they are all college dropouts living with Mum and Dad that fill in empty shoes when it's that or starve.
Or maybe it's just a fake multiplication factor and I am speaking total shit.
EDIT: I definitely plan to test this out. I find mucking around with aspects of the simulation more fun than playing it normally