I'll assume you're using GNU/Linux. I've tried the following:
* https://github.com/ahodesuka/ahoviewer which is not maintained anymore and it does not support for recursive sub-folders image checking, so most likely not as good as you want.
* https://github.com/phillipberndt/pqiv you need to add couple of configuration settings and it should be all good, one enabling natural sorting and the second one is remembering the last viewed image in the folder you started pqiv form. I haven't tried implementing the latter yet but I believe that it's doable, instead I used the interactive montage mode (a.k.a. "image grid"). Keep in mind that it can do recursive loading from directories!
Currently I'm on KDE and I found gwenviewer to be good too.
On a side note, if you're looking to download manga for desktop reading, considering looking it up on https://archive.org/details/manga_library, you're likely to find high quality versions there than on the million manga online reading websites.