Hello,
I have just tested Nuitka with Scons 4.0.1 on my system, and had no issues at all. It seems to me that they didn't change anything in an incompatible fashion, the majority of changes are irrelevant to Debian (Windows stuff), and dropping Python 2.7 support, which is now irrelevant to Debian testing/unstable too.
Nuitka is doing some monkey patching to disable some tools from loading (reducing start up time), and workaround some limitations, none of that has broken in any way it seems.
Yours,
Kay