It's not at all unusual. I noticed several years ago that the indexes of Marine Deaths seemed to contain mainly deaths on merchant ships, very few from RN ships. The indexes from 1910 onwards were typed, instead of handwritten, so it is quite easy to run your eye over the pages and see that there are only a very few HM ships listed. The numbers increased during the war years, but a few spot checks show many naval deaths on the Commonwealth War Graves Commission site that are not in the Marine Deaths indexes.
So I looked at the legislation, but found that the 1874 Act for the Registration of Births and Deaths contained virtually identical provisions for the registration of deaths on Merchant Navy and Royal Navy ships. Notification was supposed to be sent to the Registrar General of Shipping and Seamen, or to the Admiralty, for merchant and RN ships respectively. The details were then to be forwarded to the Registrar General of England and Wales, Scotland or Ireland as appropriate.
I think the operative phrases must be 'in such form or manner as the Board of Trade may direct' and 'as the Commissioners of the Admiralty may direct'. I can only conclude that the Board of Trade chose to direct, and the Admiralty chose not to. If someone who knows about the inner workings of the Admiralty can shed any light on this, I'd love to know!