Amazon seems to be able to tell most pirate sites, but people do get emails about books in KU and other sites. From what I've seen, if you email them back and say it's a pirate site and you've sent a DMCA, it's cool. Of course, sometimes it's not, but it can be fixed.
The thing with Amazon is they are running bots. The only real people doing anything tend to be ESL folks in other countries, who seem to act like bots. Half the time they don't know anything, which is why you have to reply to emails and keep at it until you hit an actual person who knows what's going on. So yeah, stuff happens. Doesn't make Amazon evil, just kind of dumb for expecting bots and barely-trained people to keep the shop working right.