Doesn't make sense. Implication: USG was listening to GG's Skype conversations, heard him say he would send big encrypted file, USG stole laptop. But GG says he never did send the big encrypted file. So they're supposedly spying on him, but not well enough to notice the non-transmission of the encrypted material.

You assume that they have full access to all comms in and out of the system; it's entirely possible that a transmission could have happened outside of a monitorable band (for example, mega.com).

To those without the key, an HTTPS download of a porn video is entirely indistinguishable from a tarball of state secrets.

state secrets steganographically embedded into porn videos. Poor NSA analysts forced to sit through hours of it trying to discover the hidden message.

Perhaps they didn't want to take the risk that the file somehow got past them (they failed to detect/recognize it, or it was sent another way (courier, etc.)).

Maybe there was a transmission of encrypted material (from a third party, something completely unrelated) and since it'd be difficult to determine if it was Snowden's they chose to take it anyways. (this is all, of course, presuming that the USG was responsible)