Personally, if I can't find a ship, I just go to that one screen that lists all your planets and ships and scroll through till I find the one I'm looking for. It might take a bit of time if I have a ton of ships, but it works for me. I never felt the need to use coordinates, as in a small galaxy, I'll memorize where everything is, and in a big one, I don't even bother to memorize more than the necessary areas, such as major production planets, or areas that I plan on invading.