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.
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.
Generally though, if you're putting something into an alcove and want a fitted look, you'd build the box undersized by some amount (1/4" to 1/2" depending on how square and plumb the walls of the alcove are), set the box in place, and then scribe a face frame to the walls.
Drawer boxes tend to be where you have to work to the tightest tolances. Side mount drawer slides don't have a lot of allowance for the drawer to be undersized and basically none for it to be oversized. Under mount slides are a little more forgiving, but I definitely still account for my actual material thickness on them. In either case, you're definitely building the drawer boxes to the as-built size of the opening they're going into and not the platonic ideal opening from the plans/drawings.
[0] Yes, I know. Slightly more than that, but this is woodworking tolerances.
This doesn't work great for what the previous poster is asking about, where something needs to fit into a specific space (the comment about scribing a face frame is mint though), but what I typically look for when I'm building things, whether wood, metal, 3D printed, etc, is to try to find the critical faces and let everything shake out around that.
For example, in the side-mount-slide drawer box situation, you've nailed it: the spacing between the exterior face of the drawer and the interior face of the carcass is critical. What I personally would do for that situation would be something like:
- cut rear carcass rails and drawer front and backs precisely with exactly the right spacing, and probably a few temporary front carcass rails that won't be part of the finished product but can be clamped in place for lay-up
- the drawer sides and front/back get dowels that are drilled referenced to the outer edge of the drawer front/back and outside face of the drawer sides
- a slightly oversized dado in the drawer front/back/sides so that the bottom doesn't need to be made as precisely. It can still fit snug in the slot, but if it's a little oversized or undersized relative to nominal, it's not the end of the world