Of course it does. Be discreet and don't draw attention to yourself in doing so - it's not really something you want to do when you've got the floor - but if you're not comfortable, you're less focused.
I dunno, I'm pretty sure sticking my hand down my pants to adjust my junk is never appropriate in public. I mean, I've done it if I thought I could get away with it, but I'd be pretty mortified if anyone ever let on that they caught me.
Yes. Being comfortable in meetings most likely makes them more productive.
There are limits, such as nudity, which can be distracting, but it's about being reasonable, and unfortunately different people draw that line of reasonability in different places.