Am a furniture maker, professionally. Do mostly hand work or at least more traditional tools, but use CNC with some regularity for jigs, templates, and the like.
If you're CNC cutting parts that need to fit together, you need to measure both your plywood and your cutting tool with digital calipers to the thou. Freud's 1/4" upcut spirals (available at Home Depot) are pretty commonly .245" rather than .250". That's enough that things don't fit.
Yes, I've been burned by this.
Also, if you're just making through cuts on your CNC, reference the bed for the Z-axis rather than the material surface, and a few thou either way doesn't matter.
I'm not even thinking about that kind of precision work.
For a basic bookshelf, the space might be constrained. Say I need the outside dimension to be 24.5" wide. If I'm using 3/4" plywood, do I model it so I have 23" wide shelves or 23-1/16" wide shelves?
Or is it irrelevant? Do you build the box first, then measure and cut the shelves to fit?
The more I think about it, the more I'm concluding that you use 23/32" and then do a lot of measuring and adjusting as you build. Taking a cut list and cutting everything ahead of time is probably a bad idea unless you know your plywood is exactly the right thickness.