The technology used on the Dragon, most of all its power plant that gave unlimited power to afterburners and guns, was too expensive for mass production. The Dragon itself in the end would be absurdly expensive per unit
Another big thing is that the Dragon became somewhat of a symbol of the evil within, which Confed didnt want to keep around so that people remembered their best officer had caused such attrocities for the good of humanity, and no one noticed
On a last note, cloacking do exist in ships in wcp. there is a cutscene that was cut off in which, I believe Maestro, says the Nephilim seem to be able to see thru their cloaking. the scene was taken out because Stilleto said "shit" or something like that