Wait, can't merchants hire mercenary companies and have their own ships? Surely SCTG has some muscle and I think that once guilds get up and running, there will be an actual need for some private soldiers to protect the stores, assets and convoys. Obviously, its all up to the ruling powers whether merchants can have soldiers under their control, but I don't think that hiring regiment of light infantry to be split and sent all over the country to act as corporate security is that scary?
Merchants can hire their own ships no problem, and there are already rules for merchants hiring mercenary
guards for convoys (who refuse to attack on principle/they're not getting the danger pay). I
will make general mercenaries available for players who specifically search for them, but you can expect all the problems that mercenaries presented historically (high rates of pay, poor nerve, tendency to backstab...)
So yes, merchants can rule the seas relatively easily, but their chief problem is manpower. Unless, of course, they take to slaving the coasts...
Edit: In the system rebuild, if I go through with it, manpower will be used to power industry and farming as well as soldiers - so taking away manpower will hurt your economy. Slaves will allow you to boost your manpower limit quickly rather than waiting for it to regenerate.