Sorry Hikiko Hime, but there is official material that shoots holes through your theory.
But first, the reason why the Hakurei shrine is a rundown place is because Reimu is trying to fix it up. Her ability to float has allowed her to walk across a river unknowingly without getting her socks wet because the fish jumped to allow her to walk across as the three fairies noticed when they tried to trick her into getting her socks wet. To add to that, Kasen Ibaraki made sure Reimu knew she was fighting someone because she bet on the opponent and knew Reimu would likely lose if she did that. Thus it can be assumed that the more Reimu tries to do something the worse that something gets done. The shrine is also in a perpetual state of poverty (Sounds like a game title: Touhou Kanraiden ~ Perpetual State of Poverty) because Reimu does her best effort to not be poor.
There are frequent (enough) events at the Hakurei shrine that it would be weird if the "overly curious" as you put didn't get into at least one gathering at the Hakurei shrine. From the annual Spring flower-viewing held at the shrine to the parties to the one time Kasen presented her right arm as a museum piece in the shrine itself; I would actively disbelieve any attempts made to say that the Hakurei shrine is not a social gathering place for Gensokyo. Especially because Immaterial and Missing Power's incident revolves around there being too many parties at the Hakurei shrine.
Yukari is also not the only one who can freely travel between Gensokyo and the outside world, Kasen Ibaraki can too. Yukari even laments on Kasen not taking what are essentially sterilization protocols causing western dandelions to invade Gensokyo, overthrowing the Japanese dandelion. Okina can too, but likely because of doors on the back of humans in the outside world rather than any backdoor boundary shenanigans (pun intended) and likely sterilizes like Yukari in her land of the back door.
Reimu is also a lot more powerful than she lets on, as her last word of Imperishable Night, Fantasy Heaven, is stated by Marisa to both be something she can keep up for until the enemy is defeated and that she can do that technique whenever she wants. Something she can also do in Scarlet Weather Rhapsody and Hisoutensoku. So it would be a stretch to say she can't deal with any potential unshackling of the true power of the Hakurei shrine's Kami.
Though I do agree with the thesis that Gensokyo is the Kami of the Hakurei shrine as I see no issues it poses or can pose to already established canon that I happen to know of. For as far as I'm aware too, the Hakurei shrine does not have a special building to keep the holy object safe, suggesting that the object in question is either an ethereal thing or too large to steal; both of which fit Gensokyo to a T.