Here are some of the tools that can be used to create "2d"* images for a VN.
Illusion games:
- "cel shaded anime style" Koikatsu and all it's predecessor and successors
- "3d anime style" Honey select and all it's predecessor and successors
3d rendering apps:
- daz3d
- blender
3d Scene players:
- VAM
Lewd Modded games:
- sims3 / sims4
- skyrim
Photo/video images:
Realporn screenshots
Realporn screenshots with hand over-draw
Realporn screenshots with AI redraw
Tools:
AI image generation
Actual 2d drawing apps:
Windows Paint
Paint.net
Photoshop
Krita
Hand drawing and scanning it
WARNING: "Well akshually" section ahead.
All things you do on a computer (with exception of VR displays and some very exotic persistnce of vision/holographic display devices) end up as 2d, because that the view device is a 2d monitor.
Koikatsu is not a 2d game engine, it's a 3d game engine. The "rendering" code transforms a camera view of the objects in a simulated 3d world to a 2d plane (the view displayed on the monitor).
Koikatsu (and all the other non-raytraced render engines) uses various shortcut tricks (phong shading etc etc etc) to output approximately correct lighting fast enough to give the player an impression of realtime motion (30+ frames per second).
Daz3d, Blender, more fancy 3d app engines use raytracing for which results in "closer to real world physics" lighting and surface reflection. This process is generally far too slow for "realtime" rendering, it's more like 0.5 fps to 0.05 fps.