I’m surprised this has gone unanswered for 2 days 😛 – the short answer is yes, if you queue into am instance with other players with Miqo running on the other account, it will be noticeable.
The long of it: Combat assist only handles the rotation – and only up to level 50 at the moment. It doesn’t handle dodging any mechanics, it doesn’t handle movement outside of positionals, etc. You would basically have to be moving both characters and still handle everything else on character 1. You *could* use follow, but you would have to select that every time Miqo uses an action. And this kind of behavior is very noticeable by other people.
Having said that, it is possible to do other fun stuff with combat assist and two accounts. I two-man farmed Turn 13 with Miqo DPSing and healing on SCH while I ran WAR, and it was a blast. I just set her to follow quickly during the divebombs and everything else was a breeze. Also got my Domitrix title from Turn 9 savage doing that with both Miqo & I as SCH’s. The idea is you just get Nael down in health a tiny bit and just heal through all the damage until she starts her enrage while still in phase 1, and then burn her down while healing and shielding her enrage blasts. So you just leave Miqo to do nothing but heal and it’s super easy. Stuff like that.
So no, for your own sake please don’t use Miqo to run two accounts with other players, but please do enjoy combat assist 😛