Theoretically, they can do you all sorts of harm all sorts of ways, as the Anything-but-Amazon crowd says.
But that's theoretically.
In practice, ask yourself: "Why would they?"
Amazon exists to make money.
They make money out of your trust.
Break that trust and...
What you should be asking yourself is "...*how* paranoid am I?"
If you're AbA paranoid, you wouldn't be dealing with Amazon at all. Or even be online at all.

(I've a friend like that. Thinks not shopping online will protect his privacy.

)
If you're all, "Amazon is my friend", then you wouldn't be asking the question.
So, your next question might be, "how much effort am I willing to make use of that nice, juicy cloud storage volume?"
Me, if it came to it, I wouldn't upload my deDRM'ed Kindle ebooks (if I had any) to the cloud simply because they'll count as personal documents while the originals don't. The point of deDRM'ing them is as backup and insurance, after all. Right?
If they came from other sources and weren't originally azw, amazon isn't likely to care no matter how eee-vile they might be. (They won't care if you deDRM'ed somebody else's product after all.) If they were originally azw, a pass or two through Calibre to tweak file names and metadata might satisfy the mildly paranoid or a full conversion to .doc or .html format would suffice if you're a lot more paranoid.
It really hinges on your degree of paranoia and the secret origin of the files.
Flip a coin?