You can go with that idea, or what I would personally do is make it so that the bats can die, but when you do get hit by one it actually does a substantial amount of damage (like -10 or something like that?) The problem with making them completely immune to damage is it turns the battle into a war of attrition because its impossible to dodge all the bats he generates. You end up just trading blows till one person dies (at this point it's always me haha).
As far as the 20 hp thing is concerned, I think things are fine the way they are right now. If i can think of any point in the game that actually should be a bit tougher, I would recommend the Oblivion fight. Even though the critters are immune, you can just hang out on the left side of the screen and spam the Polaris so that you never deal with them. I would add one or two critters so that you're forced to dodge them throughout the fight, and maybe lower his HP a bit to compensate for this.
Hope this helps.
P.S. The critters in Egg Corridor are not immune to damage.
P.P.S. Please tell me where to find or at least give me a hint about the Nemesis. I know it involves that password in the dev room but I have no idea what the password would be haha.