Reimu is supposed to be 'invincible' because she's the Hakurei shrine maiden with a whole bunch of connected powers granted by her lineage and training. Danmaku play is just designed to balance the differences in power a little and make sure the strongest don't accidentally blow up their little pocket dimension fighting one another.
Reimu has fought without the spellcard system in the past and has very relevant powers should she get into real fights with youkai. Hell, she even has her own loosely defined invulnerability power.
Getting back to the spellcard system, there was still the issue that even if Reimu is defeated, killing her is dangerous. The system allows them to sort out their troubles and create them without worrying too hard about maintaining their home.
Reimu isn't invincible so much as she has the odds stacked heavily in her favour. Gensokyo is where she's at her strongest but I'm sure she's pretty strong away from it too. Last thing Youkai want is to open the path for Reimu to start just killing them, she already cares so little for youkai in the first place to the point she doesn't even consider it theft to take things from one.
tl;dr - Reimu is top bitch in a setting of bitches.