If you shoot the power-ups the bubble surrounding them should pop. At that point it's considered collected and will act accordingly (either by giving you a tripleshot, points, or repairing your hull). Were the bubbles not being popped when you shot them, or were the power-ups not actually doing anything?
Also thanks for the feedback! I'm glad someone finally noticed the shop, its script is an unoptimized mess that's barely held together with hot glue and hope, it got so bad that I considered scrapping it for a while.