Of course it's not the smartest choice for that purpose, because there might be chip-to-chip differences. And environmental factors like temperature could affect it as well.
But who knows what people wrote after Bleem PS1 emulator was public?
So have metastability issues (or other HW bugs) ever been used for copy/emulation protection?
I'm not aware of any copy-protection scheme on the console that would target specifically emulators. I guess Bleem was not big enough a threat to warrant specific protections?
Besides I expect that Bleem, in order to run full speed on the underpowered hardware of the time, must have had terrible accuracy and therefore must have employed a wealth of game-specific hacks to get around issues. As such I expect that if they had decided to emulate your game they wouldn't have had too many issues reverse-engineering any trivial metastability-detecting code to implement an ad-hoc hack.