I just tried it yesterday on one Django project. The DB migration failed. It seems that when doing DB migration, Django actually looks for .py files which don't exist anymore with nuitka.
It's possible to build shims that support "import module if running interpreted python; just point to already-loaded/compiled code (or eval a string, ew, but if you must) if not", but many large projects do not do that. It is likely not too painful to implement/send a PR for though.