The most common method used is pad printing, where a silicone pad with the desired pattern is pressed against the shell usually by an air cylinder. The machines are relatively simple, as the parts tend to be loaded and unloaded into the fixture one at a time by an operator. Multiple colors require separate pads and may be done across multiple single pad machines. Sometimes turret or linear mechanisms can move the workpiece between applicators.
Making and maintaining the pads and running the machines tends to be labor intensive, adding to the reasons why our trains tend to come from Asia.
Another option, which I believe Lionel uses on their US made products done in Concord, is UV inkjet printing. The process is pretty much the same as what happens on a home inkjet printer, except that the inks and the heads which apply them are much more expensive. I used to work for a company which built machines around a Konica/Minolta uv print engine and the heads were over 2k apiece. But, you can put 4 heads inline and with 4 colors (cyan, yellow, magenta and black) and really good motion control you could do full color prints in 1 pass.
The head assembly moves over the work in linear passes like a home printer does, just on a much larger scale. The inks cure quickly under a powerful UV lamp which can move with the head assembly or be a separate stage of the machine.
The equipment is much more expensive, but with multiple shells in the fixture and full color in only 1 pass it's an option when your labor costs tend to be higher.
There may be other methods, but these are the only options I know of for applying print to the irregular surfaces of a body shell at production rates.
Nick C.