I focus it on the hoses and plastic, but I'm sure some does get on the paint. I use Four Star Spray Wax on engine bay paint when I want it looking good like that.
According to the directions you can spray the CD2 on anything in the engine bay including paint (except the alternator and some other odds and ends read the label before using). Pretty much everything inside the engine bay got sprayed in the two cars I did. This includes the firewall and other painted areas.