Its possible that his kitten-hood illness was caused by a virus, like the Feline Herpes virus or similar. These have a tendency to cause horrible illness inistially, then lie dormant in the cats body for the rest of its life, and flare up again on occassion with much much milder symptoms, like watery eyes or light sneezing. That would be my first suspicion. Cats can get hayfever like symptoms from allergies but its pretty rare. If you want to confirm a diagnosis, when he is having a watery eye day, take him to the vet for a Feline Upper Respiratory PCR test. They will swab his eyes and throat and sent it to a lab to determine what viruses may be present.
or
you could just treat it like it is herpes which won't hurt anything. Since its a virus, there is no cure, but supplementing his diet with L-Lysine helps lessen severity and duration of symptoms. They make Lysine supplements for cats that your vet may carry, or you can purchase OTC at a health store.