In case anyone else finds this, I ran into this same error, and solved it by:

(1) removing ninja, ninja.bat, ninja.py from depot_tools (I just put them into a temporary folder, so I could move them back if it didn't work)
(2) copying ninja.exe into depot_tools

When I ran the cmake Ninja command, I got all kinds of errors about certain files it wasn't able to find, but then running ninja aseprite afterward worked.

I don't fully understand why this works. The best I can tell, ninja / ninja.bat are wrapper scripts that call ninja.py, and ninja.py is a wrapper script that searches PATH for ninja.exe and calls it, so by copying ninja.exe there in the first place, you're kind of cutting out the middleman?