Squid,
Before you make this decision, I would refer you to Service Bulletin # 49-24 dated May 20, 1949. It is directed to "Distributors and Dealers".
It reads as though this was not a factory installed part, thus was probably not drilled at the factory.
Here is the major portion of the bulletin...
In order to reduce the vibration of the spare tire on the Model CJ-3A Jeep, a hard wood spacer can be installed on the side of the body as per the attached sketches. The thickness of this block depends upon the size of the tire used on the vehicle, whether 7.00-15 or 6.00-16. The thicker block is used with the 6'00-16 tires.
Where vehicles are used in rough territory, it is suggested that you interest your owners in the installation of this vibration dampener. It can be purchased under Part No. 671158 for the 7.00 tire and Part No. 671157 for the 6.00 tire, or made locally and installed in accordance with the template attached, by using the following parts.
The actual service Bulletin can be found at the 2A Page. It includes a couple drawings, including a template to use for proper placement and drilling.