I mean, if you're a God Bird and someone built a tower specifically as a shrine to you to worship you, I can think of worse places to hang out.

That said, it's not like they roost in them all the time. Even in HeartGold (wherein Ho-Oh is the storyline object of your pursuit, and Ho-Oh is in the Bell Tower and doesn't have the whole "fucked off to the Whirl Islands after Brass Tower burned down" thing going on as an excuse) getting Ho-Oh to appear at the top of the tower is still something that requires the Chosen One, the Rainbow Wing, and a bunch of totally not kitsune kimono girl shrine maidens who claim to have been at this unsuccessfully for ages before you finally got it.