I've never had a scavenger station or market stall self repair, although I suspect that sometimes that damage is caused by my own defences.
Especially splash from missile turrets.
When I'm there during an attack I take more damage from friendly fire than from the foes.
The same things happens with the settlers. They take more damage from the defences than the foes.
When hit they all fall down for a while, get up and some limp home.
I have seen a few named settlers die though and their naked corpses hang around respawning their possessions.
Also initially when i didn't bother with settlement building some settlers disappeared from settlements and at some, upon later return, I found corpses of the named settlers .
From my experience when the PipBoy shows a discrepancy many times something is actually wrong.
Not always but it can be a subtle thing like a new settler arriving causing a bed situation in those settlements with pre-existing beds.