Well, the game wouldn't crash... But it'd be impossible for projectiles/beams to collide with the ship so you could never destroy it (unless you knock down its shields and finish off the hitpoints with the same hit). Black parts in the alpha channel are merely non-solid, not "invisible" if there's something in the RGB channels there... Non-zero RGB with zero Alpha gives you the transparent glowing effect used for the ship lights and Kawangi reactor glow.
This would allow you to create an insubstantial / indestructable "ghost ship" which could be really interesting
(I think it'd only be destroyed by the bomb or a nova if you don't give it a shield)