Well that is a bit shocking! All the holes I've seen from wood-boring insects (carpenter ants, powderpost beetles, carpenter bees, etc.) are quite small - carpenter bee holes are fairly large, but only about 1/4". Those appear to be about the size of a nickel. Is that right?  Teredos (a.k.a. ship worms) can make very large holes, but only in marine environments.

Did you try to patch one of the holes (the one in the center)? Given the size, I have to ask - any chance these are loose knots that have fallen out as the wood has dried? The knots would be on the ground under the deck.  Or... given that it does look like one of the holes was patched - perhaps the manufacturer of the decking patched the holes and the patch has fallen out?

The only insect I can imagine making a hole that size is the giant root borer - see https://extension.oregonstate.edu/pests-weeds-diseases/insects/what-are-those-worms-my-firewood.  I have not heard of these boring into dry wood (vs. tree roots or green firewood) but there is some indication on the page I linked here that they can damage framing lumber. 

Well that's good news - glad to know it's a normal phenomenon.  You're right though.  That is quite odd for them to fall out now.  Enhanced drainage - a plus!