a few more things i just thought about
Moco Moco Friends is a... well, relatively overpriced jrpg that i think is fairly cheap relatively compared to most of the full price releases anyway so idk maybe to also consider
Virtual Console has some neat stuff i guess like the gen 1 and 2 pokemans had online or something iirc, there was also some weird exclusive stuff like Murasame Castle and Summer Carnival 92 Recca (maybe first bullet hell). there's also just kinda rare stuff too like one of the Shining Force game gear games or the Legend of the River King gbc titles (fishing games with some light jrpg battle elements on the side worth the low price of admission imo)
I know you clarified you weren't looking for ones with physicals but i figured i'd add that stuff like Etrian Odyssey titles are dirt cheap in half of its cases (also megaten stuff) and all of those are already hell to get physically. This applies to 7th Dragon III too (and also Radiant Historia's enhanced ver).
Also I nearly forgot but Chase Cold Case Investigations is even cheaper (and actually eshop only)
Also also it's jank as heck and I haven't personally played it since it's also not available in my region (why did australasia miss out on a huge chunk of even the stuff europe got ugh) but Family Kart 3D is... a vastly inferior kart racer to MK7 and even Sonic All Stars Racing Transformed (which is quite not good on 3ds tbh) but not the worst out there probably and definitely on the very low end price-wise
Also also also I completely didn't even know it was a thing until right now but I guess arcsys made some other eshop racer that wasn't released in pal regions called VectorRacing too huh no idea if that's any good (it's also very cheap though)