Hmm, well, it would certainly make the awards more inclusive for those creating a limited run comic. If this goes ahead, I'd suggest that it must have a definite ending (preferably even a "the end" either in the comic itself or the author's comments, to be sure), that was envisioned from the original inception of the comic, rather than hastily tagged on when the creator decided they didn't want to do it any more. There would have to be some limitations - a minimum number of pages posted in the 12 months leading up to the awards, for example.
I think a limited run comic that's been started but isn't complete wouldn't qualify if they finish after the awards take place (or after nominations close), but would for the following year.
I don't see a resources problem because in theory, they judges would have less to read than for any other category except New Comics.
It's just occurred to me, however, that there might be a problem in terms of updates. Imagine there's a limited run comic that's 120 pages. If updated weekly, that's just over two years - would that qualify for the award? But if updated daily, that's four months, give or take a few days. Would that qualify? I think for this kind of award, we'd need a page limit rather than a time limit.