You don't have much/any meat inside the shells but it'll impart some of the flavor. I'd recommend simmering to make the stock and then adding some mild flavored seafood afterward to it to compliment it. 
Some say add vinegar to get the calcium from the shells, but I think your way would be better, no matter that the cooking would be longer. Adding that seafood at the end like you say, it could even be added raw right at the table like a pho or cross-bridge.
Personally I'm not completely sure about any cooked food, but cooking shells and bones is a fairly healthy way to get important hard to get amino acids and minerals and fill in nutritional niches.
