Yeah, they may not have been the biggest navy in 1939, I'll conceed that.
But I don't believe that waiting a year would have allowed the U-boats to significantly decrease Britain's naval strength. After all, lets look at what actually happened.
--Britain starts the war with 15 capital ships, Battleships (BB) and Battlecruisers (BC).
-1939. One battleship lost. One to subs
-1940. No battleships or battlecruisers lost.
-1941. 1 BB 1BC lost in European theatre. One to subs. 1BB 1BC lost in Asian waters.
-1942-45, no capital ship losses.
http://www.naval-history.net/NAVAL1939-45RN.htm
The Queen Elizabeth, King George V, Royal Sovereign, and Nelson classes all mounted 14-16 inch guns in their main batteries. (Fourteen ships from these classes survived the war) How many shots from 14-16 inch shells would it take to sink a troop transport? If even one of these ships got in among the invading fleet, it would be total carnage. Once there, U-boats would have a hard time interfering because of the danger of hitting their own ships with missed torpedoes. And, faced with an immenent invasion, the Royal Navy would have stopped at nothing to stop it.
Submarines were commerce raiders. They found it difficult to sink warships when the vessel was aware of them, and were certainly unfit to provide active cover for a land invasion.
So, I don't think submarine attrition alone managed to cripple the Royal Navy, and the Nazis were pushing sub warfare about as hard as they could have.