What are the disadvantages of using them, compared to the "normal" signaled intersections? do they cost significantly more?
Free flow intersections take up a lot more real estate due to the wider curves needed for the higher speeds. Every time traffic crosses the roads need to be put onto a different grade. This means bridges and ramps to lift the traffic to that grade and back down again. Ramps (and the levies they are built on) also take up space and moves interaction with the main roads away from the actual intersection.
If traffic flow is not heavy then a simple priority regulated diamond interchange with just single lane traffic all around is more than enough. With a little forethought adding a third lane on the bridge to allow for left-turning traffic to not block other traffic will help flow for not that much extra cost.