I've always just left the holes open, since often you can get as much damage from tomato/pepper/eggplant plants sitting with wet feet. Yes, the water does come out, but the soil gets saturated....I used to have my plants with shallow rimmed plates underneath. When it is searingly hot and dry, it can help - but that extra water gets used quickly, and the plants really did no better or worse for them. Good aeration is always best for a healthy plant.
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Craig
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