You are perhaps mistaken here. The FAA allows passengers to take guns on planes provided they are documented and secured and checked into the hold. What the FAA is concerned about is people being personally armed on planes and there are obvious reasons for that.

They are largely unrelated to the reasons countries might have for being nervous about merchant vessels packing anti aircraft weaponry.

You are I think getting lost in your analogy and in the process conflating two different things:

- the reasons countries might want to prevent people from entering with weapons

Vs

- the reasons countries might have for being nervous about armed merchant vessels in their navigational waters