Ships do pay off. My ships have forced the Ptolemaioi to accept a pretty cheap ceasefire treaty... I had them blocking their main trading hub, the Eastern Med.

Before:
3 to 4 full stacks of annoying elite units, all those Klerouchia pikemen and the like.
After
Just one stack of elites, and that is a garrison.

Why? The Ptolemaioi didn't have the funds to replace units.

Conclusion:
Ships are terribly effective against enemies whose main source of income is naval trade.