Holy dickballs am I ever late to this thread's party.
But anyway, since I've started simming, I've found no evidence of the Penalty Shot attribute adjusting automatically. Only the Morale does as far as I'm concerned. So unless you're actually referring to these sliders (which are another thing I'm not certain actually do what we've always thought, but that's a different bag), I have indeed been manually adjusting them casually, more or less for my own entertainment.
At any rate, it's a null point. You'll notice that back in the day, on one of the more archaic versions of STHS, PS wasn't even an attribute that existed. Ditto for Endurance. It does now with the newer versions, but considering we still run off the original 1.1 setting, I'm inclined to believe that the PS (and EN) stats literally do nothing, much like Coaches. I literally adjust them for shits and giggles, very roughly based on age, position, scoring, puck handling, and whether or not the player is European (especially Finnish).
I could just leave them at 40, or 99, or whatever, but that added extra bit of monotony would literally SHATTER MY MIND AND DESTROY ME AS A PERSON. Just kidding. But seriously, it doesn't make a difference, except probably in the ASG and occasional pre-season. I'd be willing to test/prove it one day, perhaps in a month where I'm not fully submerged in a pitfall of alcoholism.