I admit, this may seem like a nit-pick, but Tony's movie references are so much a part of the show that when they miss one as obvious as they did in this episode, it's actually a big let down. When they got to the point in the show where we discovered that Silvino, the "big bad guy" they were hunting for, had been in the hospital for quite some time and that someone else had been using his name to run his empire, the very first thing I thought of was "The Princess Bride." In one of the most oft-quoted parts of the movie, Weseley reveals that he's made his riches as "The Dread Pirate Roberts" - and that the secret to having done so was that people responded to the *name.* No one knew what the "real" Dread Pirate Roberts looked like, so when Weseley took over, no one knew he wasn't the "real" one.
That was the same basic concept here - Perry took over for Silvino after Silvino became incapacitated. Everyone responded with the same subserviance as they had to the "real" Silvino because no one knew he was out of action or that someone else was using his hame. With part of Perry's actions as Silvino being piracy, him not making a "Dread Pirate Roberts" reference is almost unforgivable!
Aside from that, however, the episode was a lot of fun. I especially loved the scene where Ziva set herself up to be able to position herself so she could take out the two bad guys who were coming into the safehouse via two different doors. That was just exactly the kind of think I'd expect from Ziva (or Major Casey from "Chuck") and it was hilarious. It was also kind of fun seeing Kort again, knowing he got his chops busted for the whole "Frog" deal and trying to work his way back up the ladder. I still wonder what's in the file he gave Gibbs on Vance, though!