Yes, they will be a bit slower, but not enough to make a bit of difference. Arrow stability is more important anyway. I have shot just about every combination and find that there is not a great deal of difference as long as your arrows are well tuned. If you see a difference in flight, you probably need to check your tune.
Lately, I have gone back to three fletch because I see little difference in arrow flight, and I can save one feather per arrow. I also see no difference in arrow flight between cock feather in or cock feather out. I shoot cock feather in because my feathers don't wear out as fast that way. In the heat of the hunt, when the adrenaline kicks in, the deer will never know the difference.