Laurent,
I get the impression that the USN intended use of the JB-2 Loon was based on a different philosophy to the USAAF B-29 bombing effort.
My theory - think of it as a extended range shore bombardment during and immediately after a beach landing. If a target of significance was discovered 100 km inland, it would be beyond 16-in battleship gun range; and routing a B-29 strike would take at least a day (arranging bomb-load, target maps, etc). The navy would probably like the operational flexibility of pounding the target with 100x 2000-lb warheads via a JB-2 bombardment. The submarine trials were much later (c.1951-52). There appear to have been plans for shipboard launch systems to carry a larger number of JB-2s (Navy KGW-1).
As an aside:
https://books.google.com.au/books?id...rocket&f=false
Google-books preview of the book "Aircraft Carrier Impero" - the Italian Regia Marina's V-1 shipboard system/pseudo-aircraft carrier.
Better book on USAAF & USN JB-2 Loon production, testing and philosophy of use:
https://books.google.com.au/books?id...page&q&f=false
...geoff