Yes, the LL Cool J honor is a head-scratcher if you look at his achievements compared to others in the music world. He was very young, and he also didn't really have the same kind of continued impact that other honored musicians have had. His songs were very "of the moment" and I think they are mostly a footnote today. After he joined NCIS in 2009, he only put out one album, which was only moderately successful.
If they wanted to choose a rap act, Run-DMC or the Beastie Boys are much more deserving.
So I also conclude that it's not coincidental that he was a star on a CBS series. I don't know if it was a condition to continue, or just synergy like Cher, but if NCIS didn't exist, he wouldn't have gotten the honor.