I use Homebrew constantly and have never seen such a thing in my life, in any version of macOS/OSX over the past several years. Not in building from source, not in casks.
Like another commenter the only security change I have is "Allow apps downloaded from" set to "App store and identified developers" -- which I'd assume virtually every Mac user on HN has also set.
Perhaps you have some kind of unusual configuration? Or there's some very specific subcategory of Homebrew packages that encounter this problem?
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.
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.
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.
You could edit sudoers so the command doesn't require a password. But really, at that point I'd just leave Gatekeeper off.
Does the method of right-clicking on an app, then "Open", in Finder work to tell Gatekeeper to quit complaining?
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.
M1/ARM code is treated more strictly than Intel, so I guess all my command line stuff is Intel.
Homebrew is a keg of worms, if you excuse the bad pun. Sadly (because it seems to be easier to get started?) many developers prefer it over Macports...
It is likely that it is not the devs prefers it over MacPorts, it is likely that end-users prefers it and the devs are following what the end-users desires. Homebrew have huge catalog of software and libraries than MacPorts.