Any object that has a factory assigned to it can be resupplied by players. They can also be slowed from coming back up by destroying the factory OR the convoy. Supplies are placed randomly within the convoy based on the damage at the destination when the convoy spawned, so if you kill an empty truck it has no effect on downtime.
Destroying a city will cause factories and the HQ to resupply slower. Destroying trains have the same effect as a convoy, except on factories/HQ instead of strat objects. There's the added bonus that destroying a train car will cut off the ones behind it. However, trains have quad-barreled 20mm AA guns like the ones found on the airfields.