The trains are always in the game. It has to do with the terrain itself using them properly. There were a number of terrain updates, changes, object editor updates, and the strat changes that essentially made most of the old maps not work properly. These had a LOT of work put into them to make sure trains and convoys worked. That was all lost, and basically (my own interpretation on it) they put out some new maps we could all enjoy but had to leave out the most time consuming bits that took forever to test and troubleshoot.
They're there. They just aren't on most maps.