I'm not seeing an issue here.
You can have up to 7 normal ship slots per national harbor.
Event and Premium Ships do not count to that restriction. Total slots is Premium Ships + Event Ships + (4 to 7 depending on national harbor slots unlocked.)
There is a total ship limit, however you can pretty much have most of your harbors completely full to the maximum and still have slots left.
For example for US. I have:
Nebraska
Montana
Iowa
Sodak
NorCal
Randall
Enterprise
Ticonderoga
Pensacola
Texas
Omaha
Sevastopol
Mississippi
Maryland
Presently in harbor. If I had the Washington, Indiana, Missouri and California, plus if I had a New York on the account that actually has a USN crew. They could also be there.
I also have 1 non-Prem/Event ship slot for USN open as well.
Which would be the maximum possible slots if you add the above together.
I have similar harbors for IJN and KM. Plus I have almost all of the Premium ships, and a random assortment of Event ships across all the nations. Many of which never have been used.
Also the total number of ships allowed on an account has been already risen significantly twice in the last year.