Depends on the sub but yeah they do. Lots and I'd go so far as to say most naval bases are the deepest port inland for protection often surrounded by private commercial businesses. Hell the shipyard most of the us nuclear subs are made is adjoining one of the nations largest ports.

They wouldn't port ban them since that doesn't actually solve the complaints, it would be exclusion from territorial waters and no one wants to do that. A. because they're safer B. Because the protection nuclear navies provide is something everyone values C. These things are usually decided between nations not generally by a sole nation.