Yesss, I don't know either if this counts as a visual novel. When the project was about halfway done, I realized they're usually in a 2D style! :)
Ooh if you want to make something in 3D, just start small! Choose any engine (I would recommend Unity, since it has a large community) and experiment with some small prototypes. Give it some time and I'm sure you can make anything you want in 3D as well! :D
Thank you for your nice comment :)