Use illustrator’s 3D. It has the needed isometric projections as presets.
Make the sides as equal size squares. The hole is a compound path with outlined A. I have only one letter, one square drawn is enough for me, I made 2 copies.
Give to the sides 3D Extrude & Bevel effect. Select isometric projections and adjust the lights as you like. Have quite light colored originals because the shading makes them darker.
Expand the appearances , remove clipping masks, ungroup all as many times as needed to be able to make edits. Delete unnecessary shapes and with the direct selection tool edit the unwanted partial slices (green circle) to invisibility. You must move the peaking corner behind the other parts. Finally group the sides to keep them unsplintered.
Select one side. Drag its corner with the direct selection tool to its place. The rest follows. Be sure you have snap to points and smart guides ON, no other snappings!
If your debossing depth is so small that it leaves the bottom visible, insert backplates. Having consistent shadows there isn’t trivial, you must draw them manually or do the whole job in 3D. That’s partially recently discussed here:
Actually setting the shadows right needs some thinking even if the bottom is invisible. The most dark side actually cannot be logically right without a trick, because its interior must be even darker. Possible solutions:
- recolor manually after expanding; it’s easy if you have no curves (=gradients).
- use shading with white in the extrude dialog and have very dark original color.
- use normal shading, but clearly darker original color, turn the light direction to leave the holes nearly black
- Let vertical sides have same coloring (adjust the light direction) and let the top side be lighter.
This is a manually recolored version:
If you want to do this in Illustrator, you still can make a 3D version, not as the final drawing, but to see the lights and shadows. Illustrator cannot handle them accurately, it simply omits those shadows that a 3D shape casts onto itself. Illustrator shades all surfaces independently.
One easy source for a 3D reference is SketchUP. There one draws the cube in 5 minutes. Unfortunately one can get it out in 2D only as a low resolution bitmap, but it’s surely good enough drawing model.