are chance rates the same in the ex area, or is the ex area better for farming omamori?

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the chance rates are the same as far as i can tell. however if you clear the extra stage and get a circle you get a prize instead of advancing to the next area and the prizes can sometimes be omamori. I have gotten 100 and 300 omamori as prizes. Keep in mind that there are other prizes to such as wild card 1, wild card 3, wild card 5, rare gacha ticket x1 and i am sure some others that i do not remember.

Also when you clear the ex stage and are trying to get the prize the number of red circles seems to stay at 2. so you always have a 33% chance to get a prize and then hope that the prize you get is one that you want (in your case omamori) this is about all of the info i think i can give. It is up to you to decide if using peronomin is worth it.