To be perfectly honest, waifu might've only in more recent days morphed into an own-goal sort of joke (an own-dunk?).
Given that it probably started over on either /a/ /tg/ (improbably enough) or /v/, though, I'd be willing it was coined with at least a shade of self-deprecation.
(Cue the internet correction agency to inform me that it actually started on reddit or wherever. Whatever. It's the Internet. Everything funny came from 4chan back when 4chan was good except that everything actually started on usenet etc etc. I'm old and I can't keep this new shit straight.)