My comic only exists because my partner ships so many of my characters, lol. He pushed me to making a romance story and I figured it'd be a really interesting and new experience that I could also learn from.
My thoughts on shipping. Hm.
First off, I trust my community of readers. I trust them to sort of manage themselves and keep each other in line, and I've seen this in action already. I'm not worried about weird bad ships happening because, well, if they do happen those people just have issues anyway and that's beyond my comic.
I think shipping is a big deal. It means those people are invested enough in your characters that they want to see them in all sorts of situations, and imagine how they'd be in certain relationship dynamics. I believe it is a totally normal, healthy, and positive thing. It's a genuine sign of interest in the characters.
I think it's also a bit weird to have any problems with it. I mean, if you don't want people to ship your characters, then don't put them out in the public for people to do that with. It's not like it's harmful or degrading or somehow an insult to the characters. If anything, it's a kind of appreciation toward them.