For future projects, I would recommend designing the slots so that the material does not allow the nut to rotate with the bolt. This width should be greater than the width of the hex bolt, but not wider than the diagonal. This should allow you to assemble the box without holding each nut with tweezers,and also help reduce the likeliness of the nuts falling into the box. If this alone doesn't keep the nuts from falling in, you might also try applying a piece of tape across the outside of the box (making sure it sticks to the nut too!) and removing the tape after the box is fully assembled.
When designing the slots, you'll want to keep in mind that all laser-cut hole dimensions are going to be slightly larger than drawn, since a small amount of material is melted away by the laser's beam. The amount of material is approximately 0.007", but it can vary depending on many factors such as the design, material type, material thickness, and the exact setup of the laser when cutting. I usually recommend a line offset of ~0.004" to account for the laser's beam width. You can read more about setting up your file for laser cutting here.
If you'd like to further discuss your design, feel free to contact us!