Often a flexible shaft on either the Dremel Tool, or the larger and more powerful Root Zip motor, with the flexible shaft. I have air powered die grinders whichI use. Smaller, cooler, and more powerful. The die grinder is cheap--The compressor and tank is not, but there are many uses for them. If possible fill the balsa or plywood (if either are in the core). I believe you said the scupper drained out aft (as it did on my 2003 boat, but to the side on my 2007 boat.
A bit vs drum sander, depends on how much you have to removed. The die grinder and a 1/4" flexible shaft will take a larger drum sander which is just under the size of the finished hole. That will give a much smoother hole than trying to use the small drum or bit on the Dremel Tool.