Even though it looks like VidCutter is no longer maintained, I have the feeling that it does get better with newer FFmpeg versions...
I replaced the built-in FFmpeg and FFprobe versions with the latest stable versions 4.2 from Zeranoe (static build), and now even when using 1024p sources it does not hang any more. And this is not only true for MP4 sources, MKV sources also seem to work.
Worth another try...