If I recall, you don't. Though, with the charge beam being as awesome as it is being out of missiles should really be a problem until the Core-X shows up.
wait, how do you refill missiles in this game against the bosses? i know the X-Cores gives X's, but the boss itself?
You can't. The developers knew you'd have charge beam, so they didn't worry about that. You can only recharge missiles from a Core-X cuz that's the only thing that hurts a Core-X.
Always keep your beam charged and always keep spinning (fire with R), since pseudo-screw attacking lets you go through Nightmare's arms which is a huge hitbox reduction
Holding B while pressing A to SJ is really awkward for me for some reason. I tried DS, DS Lite and GBA SP, but it doesn't make a lot of difference. Also, sorry, I meant to ask whether there are any significant differences between 1% Normal and Hard at all.
and remember when nightmare is flying around, try to go all the way to the right, (not all the way, but just close), because if you don't, and you want to get back on the grappling thing-gie on the left side, he'll fly one more round before settling down (perhaps more?)