I'm not sure if anyone ever played Earth 2150/The Moon Project. I was taking my idea of cloaking from that game. Basically one race could cloak, either by having a special module on the individual units, or having structures in their base which allowed for it. Of course appropriate research must take place first. The effect would be a radius type effect (so it applies the cloak to itself/around it within a certain range)
Earth 2150 was a ground based RTS and not so open as sins is. Currently I'm not sure if the idea would work all that well in sins as far as being able to cloak everything goes. It's just something to experiment with.
Combat would still be heavy, the idea wouldn't be to hide and not attack. You could attack, while being completely invisible.

. Of course there would be researchable counters to the cloak ability, such as radar stations or a radar type ability that could be permanently applied to certain ships, and therefore canceling out the cloak.
This is just a rough idea, it may not even be practical.