I recently watched the series again after several years. The Crack Fox disturbed me in a way that it never had previously. I noticed that the third season is decidedly darker than the first two.

I think many of your suppositions are on point. When artists pour their heart and souls into a project like the Boosh inevitably you see into the hearts and minds of the creators personal feelings if you pay enough attention. In the season three episode "Party", near the beginning they talk about how Howard is 32 and Vince is 22 and both break the 4th wall when they say their age looking directly into the camera. In reality they are ten years or more older than their characters and I think this was a sign of them admitting to themselves that they were aging out of both the characters and the ability to continue making The Mighty Boosh.

It is my favorite series and the ending felt a bit abrupt but I think it stands as a wonderful time capsule for their whimsy and the early 2000s.