I don't know if there's any meaning to the skull cube.
For the number and writing cubes, I cannot definitively prove that there is no additional meaning behind them, but there does not seem to be any evidence implying otherwise. Taken at face value, they're clearly tools for Fez denizens to stamp out numbers and letters. This is implied by:
- Each face is unique.
- Each known number glyph corresponds to one of the number cube's faces in some orientation.
- Each known letter glyph corresponds to one of the writing cube's faces in some orientation.
- The raised portions of each face correspond to where ink appears when you normally see Fez-world writing.