Well they exist until contradicted, really because of their lore background its something you would have to try hard to purposely make non-canon. If you don't like Inquestorum Dark Troopers might I suggest then Shadow Guard from SWTFU? They were made Primary canon.
There is no "primary canon." There is Canon, and there is Legends. The multi-level canon scheme got thrown out a long time ago. Currently, the canon is the six movies, TCW, Rebels, and anything published after and including A New Dawn . I've a feeling Rogue One will remove Dark Forces (and, thus, its sequels) from the possibility of canonization. So, Dark Troopers aren't even a thing anymore.
You're coming at it backwards. You're thinking that things are canon until proven wrong. That's not the case. Everything is Legends until made canon. The Force Unleashed is no longer canon. If Galen Marek ever shows up in a movie or TV show or book or comic book, then (and only then) will he (and only he) be made canon. There's no Juno Eclipse, no Rahm Kota, no Maris Brood, Shaak Ti didn't die on Felucia, Starkiller wasn't cloned, and so on.
That material is still there if you want to use it for your RPGs or something (I will continue to use The Old Republic stuff in my games, for instance), but as far as the canon stands, it never happened. After all, legends are rarely true.