Samantha,
You and HrL described the two major disadvantages: water getting in the slits and unfiltered air getting in the slits. Also, the area around the slits sometimes get a little oily/dirty.
The major obvious disadvantage is water getting in - you have to cover the slits if/when you ever use water-spray to clean/rinse the engine.
As Brad showed, the cowl-vent drain-tube should direct water away from the slits (If installed correctly). I put a removable extension-hose on my cowl-vent drain-tube to dump the water right to the ground (if/when I get anal, the hose comes off easily for shows).
