Why have boats? That's a ridiculous question.
Strategy wise, it would open up a whole new dimension of the game. "Oh no it won't, I mean, OMGZ SPACECRAFT GO OVER TEH WATER!!11" Yes, they do. They also get owned by any decent anti-air defense. Someone masses anti-air on the other side of the water? Launch a naval attack. They guard their side of the river with turrets? Ferry some ground units over. It's obvious what its purpose would be; it would make players build more than just anti-air on their side of a water body.
And the submarine idea is decent. An 'invisible' unit when submerged, but can also move at the same time. I'm sure they would add some significance to it, like having an upgrade which allows it to detect.
Now, of course some people are saying "But you can't expect water on all the mapz LOLLIEZ!!1" Obviously. Guess what? You don't use water units on waterless maps. Holy shit, what a hard concept. No water, no water units. Gee whiz.
And from a map maker's point of view, it would be a beautiful addition to the game. There would be infinitely more possibilities with UMS maps, nevermind the kind of naval-based Melee maps that would undoubtedly be made.
I like the idea. I give it my seal of approval.