It depends, to an extent, on the type of rib.
In a commercial outfit or dive rib where stability is paramount, defiantly in the water.
On a fast sport rib, probably just touching or even out. If high speed handling is key then getting the tubes well out of the water will allow greater angles of lean in without the tubes lifting the back of the hull out of the water and reducing "grip".
That's the great thing about ribs, there are all different types for all different people.
Provided you get the type that's right for you and appreciate its design features (limitations) you'll be fine.