Remember compared to you assume we are all laymen.
It would be interesting for us on the armchairs how such software even works. Is it like (ahem!) antivirus software looking for patterns?
Answer is: no, not proven to be perfect. Most source is closed for the software. There is no specification. Never been a red team trying to break it. Unknown if it’s ever stopped any threats. There is no requirement to do it, and it’s all voluntary (though pretty much all synthesis providers do it). Mostly they just hash kmers and translations thereof and scan a pathogens/functional database. So implementable in a simple KV store for the most part. The bigger problem is false positives, and most work is done in de-shittifying the upstream pathogens data.
Here’s a good paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9988571/
Last I checked all the groups charged a lot of money for access, unfortunately, and I’m not really big enough to join a group like the International Gene Synthesis Consortium :(