I think the most important thing to note is that there's a huge difference between hinting at a romance, characters not getting together, not explicitly stated romance, and queerbaiting.
For instance, lots of shonen anime and childrens cartoons, you don't have romances front and center, so it would be weird to go out of your way to point it out or get together these two gay characters more than any other relationship implications, just because they're same sex. One anime I watch consistently put a male character in the love interest shots with the two other girls, and had a highly implied gay couple in the background, and this was never considered queerbaiting because only one couple ever actually got together, a background couple in the last minute epilogue.
Yuri on Ice, falls more into never explicitly stated (although I'm told the DVD release moved Victor's arm in that episode where he jumped on Yuuri and did show the kiss rather than just imply it). And is another excellent example of gay relationships have to be shown more explicitly than het ones to be accepted. If a het couple had a kiss hinted at that strongly, hidden by an arm position, love confessions and wedding rings, they'd be accepted as canon instantly, because YOI is gay, there are some people who aren't sure. The same with Symphogear, how often do a pair of girls have to share a bed and bath, call herself her wife, say I love you, hold hands and so on before they're accepted as a couple and stop being called queerbaiting and accused of using lesbian relationships as a draw.
And that's the thing about queetbaiting. It's a conscious decision to use same sex relationships to draw in the crowds, even though you have no intentions of ever doing it. Sherlock is often accused of this, for constantly playing up to people mistaking them for a relationship and constantly teasing it but never making anything of it, but continuing to do it. Yes, shippers were a lot of the problem early on, but more and more people are playing up the shippers. Not that it's a new thing. Remember how shows you to hype a lesbian kiss weeks in advance because it was such a big deal just to get people excited about a possible scandalous lesbian relationship, only to turn out it was a game of dares or something equally pathetic? It's the same sort of thing.
As for why it rarely seems to happen in webcomics, because webcomic creators tend to be independent. They don't have to get around censors or executives who aren't sure gay relationships will sell, or that they'll turn away their more conservative audience. Much of the webcomic population knows that LGBT material is desired and will give it. Lots of the community are LGBT themselves and want to create media themselves. I'm sure there are some people who play up to BL's popularity for views with no intention of every doing anything with it except to get people interested and talking, but I think it's rarer. And possibly because there's far less money in webcomics, so people aren't driven to make things that will sell to a mass market so don't offend anyone.