Well, I still need some more theories before it would be a good story. I'm also not very experienced with writing yet, so I'm not sure if I would be any good at making a fine story. Your 'Outsiders Guide to Gensokyo' idea looks very promising though.

It's going to be hard to reach the Hitchhikers Guide To The Galaxy's humor though. The 'PNP-Theory' is an awesome name by the way

Now UFO's, when summoned they collected PNP from the surroudning area until satiated and then released more PNP when destroyed. Especially blue ones which would release up to 8 times. How do these fall within the theory?
And what is the origin of PNP anyway. What is the history of drug abuse in Gensokyo?
I'm sure that together we can find an answer.
I think I already have a theory how PNP comes to existance. Gensokyo is one of the few places in the world left with any form of magic. Considering that outside of Gensokyo (and it's adjacent worlds/countries) man hardly beliefs in magic (or even divine interference), it might be quite possible that magical energy is becoming very scarce. When the world used to be more faithful, there was more than enough magical energy for all youkai and sorcerors. They could easily just absorb the magic from the air around them to power their spells.
But now, with an unfaithful world, magic has started to decline. There isn't enough magic left for youkai to freely absorb whenever they want. The only creatures who are still capable of absorbing magical power are fairies and various F.O.E.'s. They process the magical power into the infamous PNP. So, for youkai to maintain their strength, they will be forced to hunt fairies, F.O.E's and sometimes even lesser youkai to obtain more PNP. That's why fairies swarm and are prone to attack when a powerful youkai is around: They are afraid....afraid they will be the next to be 'devoured'. Like various kinds of fish, they gather together and try to defend themselves. Sometimes they aren't capable of distinguishing the attacking youkai from other creautures in the vincinity, and start attacking them too. That's why Reimu gets attacked by swarms of fairies right before she faces the boss: They think she's an enemy too. Thus, Reimu counters the attack to defend herself.
This also explains why bosses have so much more points than you: while you were flying through the stage, they were on a fairy killing spree, getting more and more power to prepare for battle. Sometimes Reimu catches a youkai while she's still charging and hunting, resulting in a mid-boss battle. Eventually the youkai retreats, having underestimated the foe, to collect more power, before returning with far more dangerous attacks.
Gentlemen, we have discovered an actual food chain in Gensokyo! The fairies and F.O.E.'s are the plants, the lesser youkai (stage 1-3 bosses) are the herbivores and the greater youkai (stage 4-6+X bosses) are carnivores. The player characters are omnivores!
The UFO's have to be devices created by powerful youkai to easily harvest magic and process it into PNP. They are basically artificial fairies, capable of producing FAR more PNP than a fairy normaly would, and without any risks of it fleeing or attacking. What these powerful youkai haven't taken in regard is the fact that other beings might destroy these devices and take the containing power for their own!
Youkai get addicted because their biological make up had was once used to a constant nourishment of magic. They are addicted to the magic power. Now that their body's are slowly addapting to the lower amounts of magic, they release less PNP. But their minds are now used to collecting large amounts of PNP, so even though their bodies would need less PNP, they still keep collecting to unhealthy amounts. This might explain youkai's sudden jump in power between MoF and SA: They are starting to overdose more and more. Because of this overdosing, their bodies are starting to swell up to contain the extra amounts of energy. Thus the growth of youkai bodies. Maybe that's why most youkai are female: Female bodies can mostly contain more than male bodies (regarding pregnancy, breast growth etc.). Some of these side effects might also be caused by the notion that PNP is slightly corrupted magical energy, since it has been contained in fairies and other beasties. This could have unhealthy consequences.
Great, now it actually looks like a Discovery Channel documentary.