Yeah, you can't change topology using the normal sculpting tools. But using the Remesh tool you can subtract (Boolean-wise) one mesh from another, which essentially can be used to punch holes into a mesh.
Thanks. Considering doing something similar for our product and add sculpting, this is one of the issues that popped into my head when I was playing around with the idea.
- add ability to indent whatever shape is (imagine a box, i press something, new outline of smaller rectangle appears on side of a box, i click, new box appears except it lets you subtract from original box. so i can go from 3d cube to empty box. sketch used to do something like that.
I think the UI needs a bit of work, but you can already subtract shapes and also extrude 2D shapes. There is a draw tool in the bottom left menu. There is also a subtract button in the tools, it works by subtracting the selected shapes from the unselected ones.
Edit: Yeah, designed for mobile/tablets first. Pretty fun there.