If you are using glass tubing, and it goes through the hole and is cut off flush with the deck, there is no need to drill-fill-drill, but make sure the end of the tube is really saturated with epoxy.

The tricky aspect of this is that you will want to chamfer the opening (i.e. countersink lightly) or you will have a sharp edge that will wear your lines or shock cords. It's tough not to expose wood when doing this unless you have a healthy ring of epoxy around the tube.

If the boat is painted, it's perhaps not such a big issue, but a clear-finished deck will show any water stains.