I haven't seen sprite comics using licensed characters for obvious copyright reasons but I know there's folks who use a pixel style but that's really as far as it's gone that I've seen.
If anything I'd say they've been swapped out for the pre-made 3d models and assets in certain softwares like CSP or the occasional toy comics, like Lego or something. If sprite comics did make a comeback I don't know if it'd be as large as those from the 2000's or the 2010's and the characters would have likely changed.