A quick google search has a bunch of people indicating it is "free" and I don't see much a TOS. Is there anything to prevent me from encrypting my data and using this as an tertiary backup?
You can use this if you are adding something that belongs on archive.org. If you are uploading something that might belong in a museum or library, you can use this api. The Internet Archive is not for your encrypted backups.
All true. However, the question was not about ethics, it was about the presence or absence of technical countermeasures to prevent less scrupulous folks from using archive.org in this way.
Peer review. Since the files are public people will spot your abuse and report it. I reported various obvious copyright infringements over time and they were quickly removed.