does the hook for the counterweight have to go into a hole or can it hang over a dowel?
Again, this is not a scoring requirement. You may attach the counterweight any way you wish as long as it doesn't violate a rule. The specifications about the hole in the rules is to insure the counterweight will fit on your device if you intend to use the hook. If your device doesn't meet the stated specs, the counterweight hook may not fit and you will be unable to attach the counterweight to your device. Under these circumstances, you have no basis for an appeal.
Think of your "dowel" in terms of the specifications.
1. "made from material no more than 6.5 mm thick" - The opening in the hook will be at lease 6.5 mm. This means your dowel should be no more than 6.5 mm in diameter.
2. "a hole at least 9 mm in diameter" - The body of the hook material will be no larger than 9mm in diameter. There should be at lease 9 mm of clear space between your dowel and other parts of your device.
3. "The edge of the hole must be no more than 1 cm from the edge of the material" - The eye of the hook will be at least 1 cm in diameter. Your dowel should be no more than 1 cm in diameter (already limited to 6.5 mm in #1 above).