Traders have found a way to stay safe for now and make a decent profit to reinvest into other elements of the game.
However I do agree that the current situation needs refining heavily, Grapefruit suggested a good fix for the situation as it stands now, that is to allow fishing to only occur in food producing ports, if you wish to trade for higher profits then the food must be transported to obtain that. The limiting factor of a players warehouse size in food ports would determine the amount of fishing vessels you could use and once the warehouse is full the fleets that return with full cargo stop fishing and remain in dock with the fishing route cancelled automatically, which would discourage players from over fishing.
The possible future model should have the same supply and demand system as gold does with its own price structure, at this point fishing could be restricted to the new dedicated fishing vessel only, thus encouraging players to invest in the new technology to improve the rate of fish per hour. I dont see restricting who can fish and with how many ships to be required with this model as supply and demand would dictate the profits that can be made thus creating a natural balance.