Typically, railroads supply the strat factories and convoys/barges supply bases. The fewer of these that reach their destination, the longer the objects stay down. So, strafing the trucks and barges keeps base objects down longer; strafing trains keeps strat factories down longer. You cannot destroy the little buildings where trains/convoys start or end.
Also, if you flatten the City before hitting the strat factories, those factories will stay down longer. According to Hitech, he recently fixed the bug where all factories got supplied by the same train.