I also think that it's mostly an attempt by slash fans to have their m/m when they recognise the potential gender issues with ignoring/killing/bitchifying the canon female partner. Also I think that it's the new thing for self-conscious sexual libertarians and "transgressive is good" types now that same-sex attraction is a bit more openly included in canon ships.

And there have been actual cases of creators playing up three-way innuendo in canon, most notably with Nine, Rose and Jack in the first season of New Who, not to mention Simon, River and Kaylee in the final scene of the Firefly movie.