Hrm, I haven't had that experience. Sure I get a port blockaded every so often, but then I just build some ships and beat the attack back. My armies aboard ship are almost never intercepted and even if they are the AI doesn't sink all the ships (So I don't lose troops), and after the 'retreat' I'm usually closer to my intended target than they are.

The key difference between high end troops and ships is that you can sack something with those high upkeep soldiers. With the fleet you can, a few times a game when the AI is feeling chippy, maybe protect a port or blockade an enemy one and slightly reduce your upkeep expenses. 90% of the time, however, they're useless florin bleeds and their upkeep costs make it so it's cheaper to recruit a new fleet every 4 turns, as needed, instead of keep one hanging around that long.