It is not advisable to caulk a deck because 1) the caulk won't stain to match the rest of your deck, and 2) caulk is not stable. Eventually, the caulk will break out and worsen the situation. Instead, it's best to sand around any cracks or voids, turn the boards over, or replace them entirely. When in doubt, consult a deck specialist or find a handyperson near you.