At the beginning of the episode, you can see Gibbs walking with a slight hitch. This is due to the fact that Mark Harmon had a knee replacement between seasons 12 and 13. There is no need to mask the injury as Harmon's character was shot in the knee at the end of season 12.
The pier at the end is the Ventura pier, about an hour north of Los Angeles. Just a few months after this episode aired, the pier was heavily damaged by crashing waves.
At the beach close to the pier (39:57), there seems to be a shark dorsal fin in the water, that rapidly goes underwater. At the other side of the wave, you can see the surfers totally unaware of this.
The garment bag that DiNozzo gives Gibbs is made by Filson.
It's revealed by Gibbs (who been told by Mike Franks) that before Kurt Mitchell it was been other agent who was originally supposed to protect his family but he asked off of the detail because it was getting too dangerous and he had little kids.