From what I've observed, and correct me if I'm wrong, the colored shots can be destroyed by shooting them using your options, if you're the same color-- in other words, if you're red, and there are red bullets coming at you, hitting them with your option's shots will destroy them-- and being hit by these bullets will drop your magic (option) level.
Destroying an enemy of the same color as you will give you half the points, it seems, while destroying an enemy of the opposite color will give you a x2 bonus.
In other words, playing this for score is an extremely picky memorizer. :colonveeplusalpha: