I do this with my pots and haven't noticed any negatives other than you have to water in a tray or sink because water will leak from some of the side holes.
I grow in small 35 oz containers and after a grow my root ball would be hella thick and curled around the bottom. Now I get little if any curling at the bottom because the holes in the side are air pruning the roots and making them spread throughout all of the soil instead of shooting straight down and curling. If you've got the time and patience you should drill holes in one pot for your next grow and do a side by side comparison of holes vs no holes. I've attached a link to some info on air pruning if you're interested.
http://depts.washington.edu/propplnt/Chapters/air-pruning.htm