But then a Planck sphere would be smaller since it would be able to fit inside the Planck cube.
okay, but we aren't told the smallest substance is a Planck sphere but a Planck length.
We live in a 3D world, and we cannot literally have true 2d objects. Even the thinnest string (if it's in fact real) has depth.
ETA: I didn't say that to suggest a sphere is 2d.
No, we don't live in a 3D, not the way you seem to believe. The universe doesn't have a privileged x, y, and z axis, it doesn't have a an equatorial plane, it doesn't have up and down (for all we know). "3D" is just a
model useful for describing and naming points in space. Three coordinates is the minimum required to uniquely identify a spot in space, but it should be rather trivial to come up with a system that requires 5 or 23.
Since the universe (probably) doesn't have intrinsic up, down, north, west, south, east, your idea that a planck volume should be a cube begs the question: how would it be oriented?