In this specific scenario, Felix is welcome to ward his ship, but they... Won't work quite as well as they should. They aren't going to make up for not having an actual ship shield, but the wards could stave off one or two hits from another ship (or other dangerous space-things). It may also be hard to tell whether or not the wards are actually going to work, while he's putting them together.

For reference, other kinds of magic/warding might work better or worse on the ship, depending. Spells placed around doorways or protection over an individual room might work better--though that doesn't help a lot in this particular instance.