I'm thinking you hear that because most people have a rack system that doesn't use lids, so holes have to be drilled in the container itself. I imagine if you were just using the tub with a lid on a shelf with plenty of space above it, the lid would probably be the ideal place for holes. Without too much space above where you're keeping the tubs, maybe the sides would be better. Either way, if space above or around the tub isn't tight I can't imagine there being much of a difference.
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