BL and yaoi bother me for a lot of reasons, or at least most of it. The likes of "Antique Bakery" are an exception, because they're not completely unrealistic like so much of the genres.

The thing is, though, that homosexuality has been deeply implicated with shoujo since the beginning of modern manga, which is really interesting. I think some of the innuendo is just the creators keeping their hand in for the sake of it, but a lot of the innuendo in Clamp, I think, is them trying to be ambiguous about the nature of the characters' relationships.