I have an extremely small amount of 3D in hydrus, I tag it with "series:real life". I have to manually tag it, but since I can count the amount of 3D I have on one hand it's not too much of a pain.
I manage my anime, manga, and books outside of Hydrus, but I keep doujins in it. I tag doujins differently from images, kind of like how exhentai has different tags than boorus do.
One of the best parts of Hydrus is the archive/delete filter. I regularly go through my archive and trim the fat, there's a ton of images that look good the first time but that you realize you would never actually jerk it to. If you have tons of files that cannot be automatically tagged, I recommend doing so to make it easier on you.