The bigger grommet is functional but these filters are made for different models of Goldwings and some use the smaller hole as well. If the tape comes loose, it made get sucked into your carbs so I would look for a plug for it. The new filters come with the plug option.
Right GS, this filter fits many bikes and the 1200 uses the larger hole, goes to the rear in the housing, and is used for the air re-circ hose. The top housing cover also is drilled out for it. There are screens in the airbox just ahead of the carbs but I would be afraid of the tape flaking off getting pulled in. You could probably get a plug at Lowe's plumbing dept or order a new filter from JC Whitney that comes with all you need for a few bucks.
If the hole is the right size and needs blanking off perhaps you could use a closed electrical grommet ******* or failing that open a bottle of chateaux collapso and get Joyce drunk and use the cork to plug the hole.