No they don't, in fact I can explore further faster with a FC than just a ship alone, and get to places I can't get to at all with just a ship.
You see you set the FC target at 500ly, then you jump out in your exploration ship and target that same system and fly to it, scanning systems and looking at stuff as you go, it's not often I can beat the FC to it's target, all it needs is a few NSP's, a couple of ELW or WW or some biology I want to check out and it arrives before I do, so no slow down at all there because I am doing exactly what I would do if I never had a FC, and at the end of the days run I always dock at the FC and set it going for another 500ly. So I am exploring exactly the same number of systems I did before the FC in the same time, and getting an extra 500ly boost per day if I have a distant target I am going to look at.