Well, yes and no. It doesn't seem as a big a disadvantage because the average online player in most games is mediocre and you can compensate by just being better at the actual game, but in, say, a CS:GO match against half decent players you'd have no chance at all.
See, I haven't played Counterstrike in over a decade, so that particular wrinkle doesn't come up. I'm fine with keyboard and mouse, I started gaming on PC(though, when I started the keyboard was used more than the mouse), but I just feel like a controller is more comfortable.
Vast majority of people never break into the top-level of play where the control format is a deciding factor and I don't really do much worse in shooters playing with a controller than I do with KB&M.