No, because it’s easy to check if your vote has been registered. If someone threw away a ton of ballots, people would notice.

They're not thrown away in the dumpster instead of fed to the counting machine. They're discarded as invalid over "signature doesn't match" and legal nit-picking. It's another case of regulatory rules being used to stop competition instead of improving market/election integrity.

This has the same problem. I can use a webpage to verify my vote has been counted. If there’s something wrong I can see there’s a problem and what to do about it. If this was widespread it would be caught.

Again, many organizations track ballot rejections for exactly the reason you describe. It’s very easy to discover this sort of behavior.