It doesn’t take long for mold to grow on empty beer bottles. Considering beer bottles get returned for a refund, you have to assume that the brewery will make an effort to reuse as many as possible.
I toured a brewery once and they showed us the big industrial bottle washing machine. They said the bottles get scanned for cracks using a laser, and rejects obviously get tossed. The question is: what about mold, which adheres quite well to the corners of the glass? I wonder if the laser also detects bottles that didn’t get clean. Or if they just figure the temps would kill everything and just be considered safe enough from there.
When the process is powerful enough to blast out the hard to reach places, followed by cleaning and disinfecting that has lead to extremely reliable outcomes across decades, there isn’t a reason to reject individual bottles that go through the process.
They most likely do regular checks to make sure the cleaning process is working as designed, as is the standard practice for any automated process. If the samples aren’t unclean, then there is no reason to worry about any individual bottle. They check for cracks with lasers because it is fast and easy to do, plus it has the benefits of not allowing contaminants in and reduces the chances of bottles breaking during filling.
On top of that the fermentation process is hostile to bacteria and other contaminants, so even if a minuscule amount was making it through, the beer will finish it off. They don’t need to be surgical instrument clean.