I did not read this above but could it just be wear and tear? Sounds a bit extreme for that though.
Wear and tear is only visible when docked to a station in to the repair tab, otherwise it's completly hidden from player when he is in space.
A 100% wear and tear dmg would give no advice on cockpit hull percentage, so OP must have taken dmg somehow during his trip or must have departed from last station forgetting to repair.