A few episodes later Hank and Gomez are killed and since this was a secret mission, no one else would have known about it.
Nope. Remember, there was another DEA officer (or similar) taking care of Huell. He didn't know about the case, but he did know that Hank and Gomez had kept Huell there.
I think it's pretty safe to say that Hank used official channels to get the safehouse setup. IIRC, these channels are designed in a manner such that there is a trail, but one that is very hard to track down (well, there has to be a trail, since government resources are being used up).
I bet that the death of Hank/Gomez is noticed by those in charge of the protection, and sooner or later a connection with the Heisenberg case is made. In which case the DEA would determine why Huell was kept in a safehouse, and take him into their custody (or free him) if they feel it prudent.