The drain holes are there to drain water...not dirt and sand.
Mud flaps are an extremely personal choice and it doesn't matter what others think of them. They serve a simple perfunctory purpose...to protect the rocker panels...and I guess for some, they also can be a cosmetic modification, too.
If you need them to protect your rocker panels...then install them. If you don't think they are worth it...don't. If you like the way they look, then install them...if you think they look funky...don't.
Totally your call...don't worry about what others may think of 'em.
Plus, there are different part nbrs for front & rear...depending on what size wheels you have and if you have the sport pkg, aerodynamic pkg, or aluminum "foot plate":