My guess it it would be two-fold: First, they are our sailors (Americans) so we can raise them and inter them if it is practical, as we normally try to do if it is possible.
If they are sailors of another country, we generally would not do that. There are exceptions, such as the case of the raising of the Soviet submarine K-129 in Project Azorian, and we gave the remains of the Soviet submariners we recovered in the wreckage a burial at sea with full and formal military honors, videotaped it, and sent it to the Soviets. I am told that while the raising of the sub raised communist hackles a great deal (understandably, but they would have done the same if they could have gotten their hands on one of our sub wrecks) the formal services rendered the remains generated a great amount of goodwill.
Of course it isn’t always possible to recover remains of our KIA, and the bodies that remained entombed inside the USS Arizona are a good example of that.
Secondly, The Hunley is a significant historical wreck, not just any wreck. Pretty much the first “real” submarine. I can see how it would be treated a bit differently.
That's a good point.