Um, well, yes, download them & hook up your reading device to your PC. It’s not that much of a hassle
What’s a pity with Humble is they offer a bulk download for these bundles, which however invariably fails at least at my end (I think/am pretty sure I must have tried it without any possibly interfering security measures in place, still to no avail), it will download just some of them, so you’ll still have to go over them by hand, now with the added hassle of checking which ones you missed.
Other than that, sorting by title should solve most of your sorting issues. Of course that does depend on whether they were intelligently titled to begin with. As with e-books though, it’s true it soon becomes hard to see the forest for the trees. Of course, working by folders may help to an extent, but only to an extent. (What of your digital photo collections, anyone? Bookmarks, for that matter?)
My days of reading & collecting comics were also largely long behind me, until as a side-effect of my gaming I’ve started dipping into these attractive bundles now and then over the past few years. What I haven’t worked out yet is what’s a good device to read them on. What do you folks use? Tablets roughly A4-sized, what used to be a standard European comic format, seem to go for around 1,000 Euros still, that is really way too steep for what should only be a casual pastime for me. I haven’t tried it yet in smaller formats, but would imagine that would be, well, small.