Standard hole diameter for corner braces

You probably don't want to do that anyway! Think carefully of what your request would mean.

A 3/8-16 thread means that the width of the bolt is essentially 3/8 inch, but what matters here is the 16. That tells us the thread pitch is 16 threads per inch. The nut being about 3/16 inches thick means that the bolt and the nut mate on three threads. A thinner nut would have less thread contact, so less strength.

If you really need a thinner nut, then it will be easiest to use a smaller diameter bolt. They have finer threads, so the nuts are also correspondingly thinner. Of course, I don't know why it is that you have chosen a 3/8-16 bolt. You may also choose a different thread pitch for your bolt. The 3/8-16 thread pitch is the standard (coarse) thread that you will find in nearly all home stores. However a more diligent search will find bolts and nuts with a 3/8-24 or even a 3/8-32 thread. They may have nuts in a different thickness.

There is a large body of information about what size furniture and tools should be. The field concerning sizing furniture to individuals and populations is called Anthropometrics and information about safety and ease of use is called Ergonomics.

If you are building your own workbench for your own use, then you should size it to yourself unless you expect others to use it. Why buy off the rack if you can get tailored for less?

Most furniture is optimized for the middle of the height distribution curve which is roughly 5'8". I got into woodworking in the first place because I am 6'4" tall and absolutely nothing fits. It's all literally 6" too short.

I used the "fall drop" rule to size my generic workshop surfaces. Just stand relaxed and let your hands fall down as if resting comfortably on a surface in front of you. It's the position you hands will just fall or drop to if you try to rest them on an imaginary surface. It gives a higher bench than the using the wrist line method above.

I suggest creating a mock-up first using whatever is available and easily resized. I used a chair, a sturdy box and books of various thicknesses. I swapped books and fiddled with the height of the mock-up until I found the most comfortable height. In my case, it was exactly 39".

You'll know it when you find your own ideal height because it just feels right.

However, shuffler is correct that different work requires different heights. The "fall drop" rule sizes a bench for use with modern power tools and precision hand tools but if you use other tools you might want a higher or lower bench e.g. heavy handsaws, chisels and planes usually require something like saw bench which is usually just under knee height.

I use a mini-bench on top of my main 39" surface if I have fiddling work like soldering.

Oh, and build yourself a custom stool and work supports at the same time. You'll be glad you did.