I can confirm if a pokemon has three possible abilities they won't have their hidden ability. I was attempting to catch a simple ability woobat and was using a kirlia with trace to check the abilities. I believe I found about 15 woobat and none of them had simple but the unaware/klutz script was about 50/50.
In response to Ame I started playing in chapter 6 and don't remember ever catching a pokemon with a hidden ability, I had just started then though so I may have just not caught one.
THOUGHT: This is just speculation but from my understanding pokemon's abilities are determined from a random 0-9 integer (I think it is a randomly generated number). If you discount hidden abilities no pokemon has more than two abilities so certain numbers from 0-9 would mean a pokemon gets one of two abilities (if applicable). I'm not sure what the script you used to make hidden abilities normal did but it is possible, if the script simply made the hidden ability a normal ability, that pokemon with two normal abilities can't obtain the hidden ability as there are no integer values that are assigned to this 'third' normal ability. Pokemon with only one normal ability would probably have the hidden ability assigned the same integer values as 'ability two'.
Essentially the game only has integers from the 0-9 number assigned to abilities 'one' and 'two', hence the hidden ability, ability 'three' can be selected as there are no numbers that will give it.
Apologies if this isn't helpful it is just a thought I randomly had and decided I'd share it. Don't know what that script you use actually does so my idea might not even be relevant.
