good vs bad waterproofing a pine planter box.

My husband bought me a nice 4'x3' raised pine planter box, "a box on three foot legs". As I was getting ready to fill it with dirt he asked me if i was going to paint it and waterproof it. I thought the pine would be fine as it is. Wouldn't waterproofing cause water collecting in the bottom of the bed? I realize the wood will breakdown eventually as part of the normal process but didn't think of protecting it because I dont want anyting to get into the vegetables I plan on growing, ie. stain or paint. I'm confused any advice would be greatly appreciated.