Yes. When you go to select a target, clicking on the ADJ or -AJ buttons will switch from Planet/Moon mode to Ships mode. Then clicking on the ++ or -- buttons will bring up a text box where you can enter the name of the ship (Transx doesn't keep a list of ships like it does for planets and moons).
A very nice little feature, I've found it to be really useful for double-checking whether I've set up a rendezvous correctly; I have yet to try hitting a station on my way in from interplanetary space, though.