FWIW, I have always set my color reading devices (PC's, Tablets, phones) to night mode with white-to-lightgrey text on black background with backlighting set low (there was a very ugly spell there when the Android Nook version recently had this "great" idea that night mode meant a grey background, not black, but B&N eventually caved in to user backlash against that notion, and now it is "black" again - as much as this type of backlit LCD screen can achieve black, which is a lot better than that grey experiment).
I use FBreader a lot, too, with that setting as it is less resource intensive, and a bit cleaner interface to my thinking, but I have to remove the DRM for that, and sometimes that is too much bother since I have to use the decrypting tools on Windoze instead of my preferred Linux PC's - annoying to crank up the Win VirtualBox, or even boot a physical PC to Windows just for that ...
There are a lot of alternative reader apps to choose from Google's Play store now that it is accessible even with the stock Nook OS - see what works for you.
Anyway, I can read comfortably for hours that way, but everyone reacts differently. It also helps to set the font large enough to avoid any kind of squinting effort (as long as that is within "reasonable" density, and not only a few words per screen of course
).