I am genuinely curious why people are singing that "I don't have that such problems in my computer!" slogan repeatedly? Some of us have that problem and just because we have the same OS and possible the same hardware didn't mean it is impossible. I wish people change that particular mindset and be aware that those problems does exist.
Obviously the problem is possible. It's happening to you. I'd like to find out why so that I can troubleshoot and fix the problem if it starts happening to me or my friends or coworkers. And really, I'd like to help you fix it, too, if I could figure out what's causing it.
I been reading other comments and as someone (xrisk) pointed out that it is Homebrew Casks which it made sense since all of the gatekeeper alerts is coming from 'Cask-ed' apps. I could disable Gatekeeper but I rather not because MacOS is not my daily driver. I rather to keep Gatekeeper active to protect itself from moronic me.
Does the method of right-clicking on an app, then "Open", in Finder work to tell Gatekeeper to quit complaining?
Additionally if they can’t reproduce, they can’t offer any advice or help.
It’s highly unlikely that MacOS behaves specially for your existence.
I can see brew trying to run x64 code while the emulator isn’t there blocking code from running in weird ways.
Alternatively, it might be that package updates fixed the packages that behaved incorrectly. Again, just a slightly educated guess.
Before I figured out the way to identify the offending dependencies I sorted the issue through signing the executable with codesign, in a way that required me to disable part of SIP. So the code was working, it was just not being allowed to run.