In a hypothetical future where sailing under flags of convenience becomes untenable, all the legitimate merchant vessel owners would rush to register in the US or China. Those vessels would still be able to sail anywhere unmolested. Outside of a few pirate gangs, no one would be stupid enough to screw with them and risk kinetic retaliation. This might increase shipping costs by a few percent.

Russia can bluster and threaten but their navy is weak and shrinking. Most of their commissioned warships never venture far from port. Outside of their territorial waters they have minimal capability to protect their own merchant vessels or interdict anyone else's sea lines of communication.