you will see where the letters were simply because the rest of the paint had faded. even if you could remove the painted letters without touching the surface behind, you will still see the surface behind.
solvent will work to some extent, however you may still have to mechanically clean the surface with either a mild abrassive or something a bit stronger. your worried about damaging the aluminum - dont worry, short of sand blasting or hitting with a grinder, the aluminum surface will be fine.
if your intention is to repaint the area where the reg letters were, I would recommend repainting the whole boat. is your intention to clean the boat down to bare aluminum?