I'm not absolutely sure, but I think that if you rename coast, sea, and ocean squares to "space" squares, the units you would classify as "deep space units" (which you would call "sea" units in the editor) might not be able to travel over the space squares. I would imagine that when you classify a unit as "sea," the game automatically looks for the terrain types of coast, sea, and ocean to determine whether or not the sea unit can traverse a given terrain square. Therefore, it can only traverse terrain squares named as coast, sea, or ocean.
As I said, I'm not certain on that but if the game does work that way, then "deep space units" would not even be able to travel over "space" squares, which would defeat the purpose of having space squares altogether. The best method would be if we could add space to the possible classifications for units, so there could be land, sea, air, and space units, but I doubt Firaxis will ever give us that ability.