if you tax people for having ships in a port that is of any significance to stop this "zerg" it stops becoming a game for a lot of people and becomes a chore to maintain them, you would out right deny any casual or part time players from ever being able to sail the 3rd rates and above. a tax on income maybe but not on the ships in port just sitting there. if/when rations come into play there is already a large negative to bigger ships, more mouths to feed.
why create a new system tax when simply having to feed your crew while at sea would keep mass thirds and above in realtive check.
in terms of a whole nation moving its muscle around to all fronts at all times, the ships still need to be sailed there, you can only teleport between outposts and only do that every 4 hours. what you may perceive to be a mass movement of the same captains to all fronts is simply different captains as in any one period. Unless sailed between they can only ever be on two fronts max and that is never at the same time.