Did you play on Casual? On Casual, damage is disabled on purpose to make sure people can see the whole game if they want to. I hope the hit sound wasn't too annoying; you're only supposed to hear it a few times per game!
Thanks for the feedback on the difficulty. I might reconsider the boss attack patterns a bit; I really wanted to make sure you saw the bullets coming back and the patterns overlapping, but I think I can get that effect without making it so hard (and maybe make it look cooler in the process).