Warships are exempt from having a Load Line according to Article 5(1)(a) of the ICLL Convention. In light of this, it's not clear why the OP thought an NES existed.
IIRC, naval vessels must meet intact and damage stability criteria developed by the various national defense establishments, which stability criteria usually exceed those applied to commercial vessels.
I know that several classification societies have developed rules for the construction of naval vessels, but these govern hull structure and machinery. I don't think the various navies have abdicated their role in determining stability criteria for their vessels.