If you're talking about water running down the channels to the doghouse when a four man truck is parked with the nose downhill, I don't think drain holes alone would do it. I don't think there's any downside to drilling (small) holes in each of the channels, but to really stop it you need to dam them up somehow. Otherwise a lot of the water will bypass the holes.
When I bought my truck there was some foam left in the channels which had apparently been under the plywood tunnel cover. Although it wasn't in every channel, in light rains it helped. For the moment, I just park with the nose uphill.
I'm going to try replicate what was there by putting foam back in the channels, then placing a piece of aluminum flat stock, cut to the bed width and painted OD, over the foam and using rivnuts to hold it in place. I will probably drill small holes just in back of this seal to allow pooled water to run out, but I expect to have to periodically clean them out because they're likely to get plugged with mud or other crud.
edited to say "don't forget to look before you drill. The fuel tank is under there somewhere"
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