Now imagine you are the worker at the CIA/NSA who decided, one day, to create Bitcoin as a honeypot project.
What do you mean as a "honeypot project"? A honeypot is usually when you design an environment that is used by hackers, for their operator to study and analyze their behavior. For example, Cloudflare
could be a honeypot, because it is extensively presented in every page nowadays, and could collaborate with the government to provide valuable information from cyber attacks.
A honeypot can be anything that attracts the entities that the CIA wants to attract so they can monitor them in some way.
I don't see how this analogy would apply to a decentralized currency that comes with privacy features, if desired. If it was created by the NSA, wouldn't they disable things like SIGHASH_ANYONECANPAY, that allow privacy techniques like coinjoin to be implemented?
Bitcoin was originally conceived as a public ledger, so that right there makes it pretty easy to track by authorities. Yes, you can use things to thwart that tracking, but a) that wasn't really invented until later, so maybe "Satoshi" didn't think of that when they first created it; b) the act of using tradecraft alone is often all the CIA needs to get the information they need.
To be clear here, my theory very much depends on the actor(s) in question not thinking everything through, and creating something they did not exactly intend to create.
It's just a theory, but I think it's the best one so far.