I very strongly support the initial suggestion!
No physical depots, trains starting at the active waypoint/station in their schedule.
This saves the player a lot of micro management, and it is absolutely consistent with the abstraction we are playing at (e.g. No servicing or tanking either). It also is consistent with the static lines pardigma: A line set up and running should not easily break. However trains comming and going to depots very often cause congestion and deadlocks, since trains suddenly take routes the player hasn't anticipated.
The only drawback is small, as mentioned above, small insular train networks, and service to small isolated bodies of water would be much cheaper.
AEO's sollution would help but is, as prissi pointed out, complicated by having to find the nearest shipyard to a stop.
A more complicated sollution could be to introduce the network id concept of powerlines, to identify the number of un-connected networks and charge the player based on the number. User example:
The player has boats on two lakes, three isolated train networks and cars on 5 islands.
At the finances dialogue she will be charged 10 times $ 1000 depot upkeep. (a mouseover tooltip would explain the costs)