I would think that if there was a need for insulation on the inside of the hood, Ford would have put it there. I highly doubt you will have any problems with your paint. I am sure Ford researched this when testing the Focus. I see no reason to give Ford a way out of warranty coverage if you have put something on your hood that doesnt belong there. I am also pretty sure that if you do have a problem with the paint on your hood, Ford will fix it for you.
Oh yeah, its Dynamat. http://www.dynamat.com/
Unless you bought some kind of copy of Dynamat.