We stayed in Clearwater in June. We stayed at Best Western Sea Wake. This is on the beach on an inlet into the bay, not actually on the Gulf, and not in the bay. The water was even calmer then the Gulf, which was visible - about a quarter mile away. There were a lot of shells on the hotel beach and the water was crystal clear. Also the kids were catching crabs and DH caught a tiny little Hermit Crab - the water was very clear. When we went up to the public beach around the corner - on the Gulf, the waves were a little bigger, but I did notice very few shells. We also could see dolphins in front of the hotel and had a pod of 8-10 manatees swim right up to DH - someone said they never see manatees in that area - so it was a special treat. There is also a Holiday Inn next door to the Best Western, all on the same beach.
Pier 60 in Clearwater - which is where the public beach is - has a great playground, and every evening they have artisans set up with stuff to sell, kind of like a little fair every night.
There are many boat rides offered at clearwater harbor, and if you want to do more serious shelling some of them went on shelling excursions.