iirc Ending 1 is always considered canon
This was a mostly baseless theory, and ZUN debunked it when he stated the Marisa B has the canon route in UFO, since it leads directly to extra. In a similar vein, it's safe to say route C1 is the canon route in Fairy Wars, since it's the only one that sets up the extra stage.
Beyond that, there's really no way to tell for sure. Elements from every ending show up in future media, so it's pretty much up in the air. One that I'd be willing to bet though is that the Jigoku route in Highly Responsive to Prayers is the canon route, since Reimu had met Mima prior to SoEW.
Cut: And yeah, if Kioh Gyoku really does take place in the same continuity, then Yuka's route in MS is canon. Also it's probable that either of Marisa's routes in LLS were the canon one, since she stole Master Spark (Yuka knows both of them in PoFV though).
That's my handle on the issue at least.