Hello malangon, you have nothing to worry about using rockwool in that type of set up. I have been using rockwool for years with my setups and never ran into any problems with root damage. My first setup below worked just fine with all plants in rockwool.
http://www.hydroponicsonline.com/for...ead.php?t=2035
Here's my upgraded setup all using rockwool.
http://www.hydroponicsonline.com/for...ead.php?t=2475
You must put hydroton on the bottom of the net pots before you put in the rockwool cube. Then you must also fill in the sides and cover the top with hydroton. The plants will do just fine because they are only getting droplets of
nutrient water.
Now if rockwool was used in a flood and drain setup you run the risk of developing root problems as the rockwool would get completely saturated during every water cycle.