whenever anyone says "no pun intended", they are obviously aware that they are making a pun so they do, in fact, intend it. so "no pun intended" is a contradiction in term.
It's a way of saying "Don't point your fingers at me, I just said it, it's your fault you got distracted."
"No pun intended" can be a) a sign of an act of sucking up to someone, b) saying something with certain words because you can't find more appropriate other words (a frequent case for non-native speakers), c) a tweaked sense of humor, d) other. I know that I use "no pun intended" in the sense of b) sometimes. I know that there is a better word to say what I mean, but I don't know it, so I use one that is closest -- and apologize for the bad choice of words.