Oh absolutely. Stones and stuff possibly getting thrown up the side of the car(I've had that happen) and things like that would certainly not be possible with some decent flaps. I will reconsider flaps after the flush kit install. I may have to after that for protection reasons.
Adding wheel spacers (ECS flush) seems to really fling a lot of crap all around the rear half of the fenders. Obviously more than without the spacers. I'm going to switch to slightly thinner spacers front and rear, to see if that helps a bit (10 front, 15 rear). Also, lowering would probably help as well as less of the tire would poke past the edge of the fender.
I think that the OEM splashguards do help somewhat. But maybe just for the side of the car more immediately and lower to the fender. Lots of crap kicked up on the hatch still.
That said, it's been all rain/snow/slush/salt/sand here for a few months now. I have hosed the car off when its not below zero, but I haven't had the car washed since installing the splash guards / mud flaps.