I don't think so.
I sank the Warspite once in April 1940 and she kept showing up in the middle of the Freetown convoys later that year.
For capital ships that have more than one ship in their class I've changed their display names to show their class (i.e., 'Nelson class' instead of 'HMS Nelson' and so on) and not the particular ship's name every time it spawns. At least that way if one of them keeps respawning the game doesn't ID it as the same specific ship by name over and over again.
For the Nelson I think there were only two ships of that class anyway, but I figure the chances I would ever sink both are so slim that if I sink one I can always pretend the other one is not
that one if I happen to run into it.
If I sank both I guess I'd just have to pretend I was playing in a parallel universe where the Admiralty just kept churning out Nelson class battleships.