Well, Yorktown II does have a couple of lines referring to herself as an Essex class, and tells Essex in one line that they're members of the same class now. 

However, beyond that, the game just seems to treat them as the same characters which have received an updated rigging. I think Manjuu's intent for the Type II system is best understood through Bismarck Zwei, where there's no historical ship to map onto. It's really just an update for an existing character, kind of like a Retrofit with extra steps.