Yes cats can be allergic to the scented cat litter.
If you have recently switched to scented cat litter but previously used non scented cat litter and your cat has now started experiencing watery eyes or respiratory issues such as coughing, wheezing or sneezing then your cat has likely been affected by the scented litter and is most likely allergic to it.
I would switch back to non scented cat litter and see if your cats symptoms improve.
Cats can also be allergic and be sensitive to dust in the air, mold, pollen and mildew.