It was interesting to hear about Deeks' dad too. I don't know if they've ever mentioned him before on the show but I was surprised to hear Deeks shot him when he was 11.
I assume he was abusive or something, since Hetty said it was self-defense. But they never specifically said what his dad was doing.
In Borderline, after Kensi tells Deeks about her good relationship with her father, he says that he's pretty sure his dad hates him.
Kensi "How do you know"
Deeks "Because the last time I saw him he pointed a shotgun at me and said, Marty, I hate you"
then he said something along the lines of how "that was six years ago, the miserable bastard could be dead by now"
It's hard to tell whether it was a continuity error, or if Deeks was referring to the incident when he was 11, and just fudged the timeline because he didn't want to open up the whole can of worms at that point.