Nice username. Love my K390 Microclean Spyderco's. I was just looking at the BRS version of the Thresher the other day and my exact thought was "if it had a thumb hole ....." .
Ok so I took the thumb stud out and used different shaped Carbide burr bits to enlarge the hole until it was the size I wanted. I started with a cone shaped on both sides till it got big enough then switched to a straighter bit. I did it on my small drill press dipping it in water periodically to keep the blade cool. It creates a lot of heat due to the enormous amount of friction. The bits I used are like this
Tungsten Carbide Burr Set 1/4" Shank 10PC Double Cut Rotary Cutting Burrs Die Grinder Bits for Steel and Wood Working, Grinding, Carving, and Engraving https://www.amazon.com/dp/B097BRDSZT/ref=cm_sw_r_apan_i_36G6FAQCHQ0GAB0ECJ53
Now what I want to get for my next thumb hole mod is a solid carbide machining bit to actually cut the entire hole in one go. Not enlarging a small thumb stud hole but actually cutting a hole. They ain't cheap though and they require a drill press. This is what I mean
Kodiak Cutting Tools KCT166681 USA Made Solid Carbide End Mill, AlTiN Coated, 4 Flute, 1/2" Diameter, 1/2" Shank, 1-1/4" Length of Cut, 3" Overall Length https://www.amazon.com/dp/B0070YYPP0/ref=cm_sw_r_apan_i_Y7QGGRZWJQ27DMWZ4ZPG
I've seen several posts from guys saying they did theirs with a dremel tool using Carbide bits. The dremel carbide bits cut really well but being so much smaller it would take a while. Would still need to finish it up with some type of larger bit like a carbide burr bit so the hole would be uniform and round.