What is the best tool to make this type of cut? T

Show us.

Not sure if you meant to post a picture but that may help. The only holes I can think of in a plyometric box would be hand holes on the sides to grab it. If you're in a hurry and doing it on the cheap, a 4" hole saw hooked up to a drill would put circular holes in the box. A jig saw or oscillating saw would work to cut out the wast between two smaller holes and make a more elongated slot. A router with a pattern bit and a jig to guide it would be the more "professional" approach, but would require a router and considerably more set up time making the pattern/jig. There's a couple ways to skin this cat.

Not sure if that is what you're talking about but hope it helps.

In all the pictures I can find, those 'small circles' are either nails or screws. Only holes I see are one on each end to be use as handles.

Cheers,
Brad

Small hole? On a plyo box? Do you mean the countersunk screw holes?

I use ones like this
https://www.homedepot.com/b/Tools-Power-Tool-Accessories-Drill-Bits-Countersink-Bits/N-5yc1vZc8xp

Agree with the other posters in that a pic would be greatly helpful. However your post makes me think of a friend of mine that makes plyo boxes for gyms in bulk. He uses a design very similar to the one John Smith posted, but since he makes a lot of them he outsourced the panel production to a guy with a CNC machine. The CNC machine has a very specific bit size which results in the corners for the tab cutouts having a small circular shape. The CNC machine won't do a 90 degree inside corner because the bit is circular.

OP could also be talking about the "dog bone corners" that are created when the pcs of plywood are cut on the cnc. That's what my rogue plyo boxes look like at least.

The holes, and cutout between, them could also be cut with a mortising bit of the desired diameter, with a plunge router, preferably on a router table. You would need to cut a smaller slot with a plunge cutting (center cutting) bit to clear the non-cutting center of most mortising bits. A jig built to locate the stock and limit the cut would help a lot if you are making several of these boxes.