Hmm, I don't remember seeing that issue before - can't think that I missed it?!
You can reduce the issue by using "start /B ...." as the command though you still get a window flash up temporarily.
AH!! Now I know why I missed it. Normally I run NR on Windows manually and that doesn't produce a new window. When you run NR as a service or via pm2, exec DOES pop up a window each time. Annoying.
I think that, to avoid this completely, you would have to create a new custom node to wrap around Windows functions. A couple of examples come from Edge.JS or the WinOle modules. You could call wscript for example from one of those modules which could then call your app.
However, if all you want to do is to run some Python code, try searching for Python in
https://flows.nodered.org/ there are a couple of nodes that claim to be able to do that.