A clean drill of a very small hole should serve this purpose and be inconspicuous. I'd say a 1/16" hole top and bottom of the inner pane would do. Airliner windows were mentioned before ... I believe I've noticed this on these applications as well.
I noticed a criticism of this project was in the stress concentrations created around the hardware. A possible solution for this would be to distribute the clamping force equally through use of a exterior "frame". The frame would not be required to provide any sort of sealing. It would simply bear the tension of the hardware and distribute it to flat surface on the perimeter of the glass.
The result would be a port light sealed by sealant, attached by hardware, and held without stress concentrations. Anyone tried this approach?