If a high flow rate is moving through the three manifolds (from the first through the second to the last), then yes it will reduce performance and the 1x9 is desired unless you join those three manifolds with pumps. You can get improved performance by overlapping manifolds in such a way that multiple connections are joined, but the only way to see full pump flow is if pumps are the only singular connections between manifolds. Getting a full 12,000/s through piping connections between manifolds requires parallel sets of underground runs. You can get away with fewer than 12 parallel runs if the distance is very short, due to the way fluid flow works in Factorio, the number very quickly climbs to 12. Fortunately, that figure is good for 100 underground pipe sections of distance (or 200 total pipes, including the manifolds).
