In Florida, you ought to do things that fit the Floridian way.
Even though Mayport Naval Base is the home port of the Fourth Fleet, the Fourth Fleet had been out on missions before.
The incident involving the blockade of the waters around Key West was handled by the Fourth Fleet.
In addition, they indeed intercepted smuggling from Cuba, and another one of their responsibilities was Atlantic cruising.
So, even though it's their home port, and though there are plenty of ships moored in the docks of the port, these are all there for repairs.
Only a few are ready to set sail at any moment.
Just before Luke's designated attack plan, a few ships set out.
That's also why Luke chose this time to attack.
They were too few in number; as long as a few ships set sail from the base, they could take control.
After all, the new Navy Commander took office and immediately blasted his predecessor for fabricating data.