Since this port fee thing has been out for a while now, I've refined my thoughts on Chinese retaliatory measures. I've thought of a very simple measure that doesn't specifically target foreign-made ships: Just charge a fee on any company that got to avoid port fees docking in the US, equivalent to the fees they would've paid had they used Chinese-made ships. For example, if say MSC had 1 ship that docked at an American port with a Korean ship and avoided $1M of port fees that they would've otherwise paid with a Chinese ship, then MSC will be billed $1M if they want to dock any ships at a Chinese port.
What this does is essentially make any company that wants their ships to dock in both the American and Chinese ports pay a port fee, regardless of the ship they use. The only way for companies to avoid fees is by only docking in American ports or only docking in Chinese ports. If they do that, they're still subject to fees at American ports if they use Chinese ships, but they won't be subject to fees at Chinese ports regardless of the ship they use.
The direct impact of this would be as such:
1) Trade cost between China and the ROW (sans US) would be roughly the same since all ships are still available to use with no fee.
2) Trade cost between the US and the ROW (sans China) would increase since all ships must pay a fee, either to the US or China, unless the shipping company has no ships that dock at Chinese ports.
3) Trade cost between the US and China would increase due to unavoidable port fees regardless of the ship used.
The ultimate impact would be as such:
1) Overall trade cost would increase slightly. The port fees per container is actually very small, so shipping companies will probably just pay the fees.
2) Most importantly, it would eliminate any incentive to purchase non-Chinese ships.
3) Less likely, it would encourage the creation of China-specific, US-specific, and inter-China/US shipping companies. The relatively small amount of port fees probably doesn't justify this, however.