You're not meant to be able to store local cars!
Have the cars you've been repairing and having this smashed-window effect on also been local cars?
Do we think this is related to the 'cars / bikes randomly breaking' issues
No, Norman, I don't believe it is.
That thread, FWIW, is about the effect that when a vehicle is removed from storage and has been previously recorded with X amount of damage to bodyshell and Y amount of damage to engine, we cannot, alas, track precisely which panels are dented, which windows are smashed, which tyres have popped, etc, etc. When we pull the vehicle from the garage we do a quick examination of the overall levels of these damages and do a bit of a 'scaled random damage' to the vehicle to represent it. This is what results in its windows smashing upon retrieval, and the tyres being popped. It's the server's 'best guess' at visually recreating SOME degree of damage that is vaguely similar to the level of damage that it had when it went it.
Long, long ago, the garages auto-fixed all damage upon storage, which is BS, but because the system doesn't give us absolute precision, this is as near as we can get. It's basically your signal as a driver that "this vehicle is a bit/a lot/very ill, do something about it!"