It sounds like you're talking about the "deep web" while not knowing how it works. BCN has not been used on the deep web in any such elaborate way. The only thing secret about the deep web is the identity of its users.
Exactly. This whole deep web, cicada 3301 connection is pure marketing.
Which brings me to "Bytecoin high level API formalized. All the services and stores are strongly recommended to migrate to it" on the web site.
Now given that as you explained above there are not likely to be "stores and services" in existence on the deep web or otherwise, the only reasonable explanation for this statement is that it is intended to falsely convey the impression that there are stores and services.
Once you start to see such clear intent to deceive, it is reasonable to ask how far the deception goes.
While this may not be a "scam" on purpose
At least some aspects of the scam were on purpose.
This is pure speculation but my guess is that the cryptonote people wanted nothing to do with the scam but still wanted to release the technology, so they parted ways with the bytecode people. This further calls into question the claimed 2 year life span.