Yeah makes sense, maybe saying they were friends was a stretch but it certainly can't look good if you're a CDR or CAPT who endorsed him for something like "leadership", right?
In hindsight maybe but many of the folks who were 'linked' and endorsed him were fellow JO's or DH's of his so nothing out of the ordinary. I worked with a guy who knew and worked with 4 spies over his career, we all picked on him for being a common thread between them all but it was nothing more than something to pick on him about.
While the profile disappearing may have been at the request of the Navy or law enforcement I wouldn't be surprised if LinkedIn did it on their own, it is a business after all and they want to minimize their exposure too.