Suppose we have a cubic unit cell. We need doping of the alloy with 5 at.%. For that we need to make a supercell for representation the doped composition. So to maintain cubic symmetry should we make a supercell uniform in all direction (like 2*2*2 or 3*3*3). Because if we make a supercell of 2*2*1 it may break the symmetry and system may not be cubic.
Actually it doesn't make so much sense to keep the symmetry (or better say shape) of supercell same as that of unit cell. As soon as you substitute some of the host atoms with new species, the local symmetry of your original unit cells changes. What matters the most is the relative distance of the dopants in each direction which ideally needs to be the same along all directions in order to enforce their random distribution in real materials. In practice this can be done in various ways using different shapes of supercells. Let's say, for example, you have a face-centered cubic (FCC) primitive cell. Based on this, you can create a 6x6x6 rhombohedral supercell with only one atom replaced to mimic a ~5% doping. Similarly you could generate other types of supercell for different doping purposes.
Adding to what Mohammad has already said, they very act of adding the dopant at some site within your supercell alters the spacegroup of your crystal to (probably) be non-cubic. You can easily verify this since your calculated stress tensor will no longer be isotropic and diagonal.
If you truly wish to investigate the effects of retaining a pure cubic spacegroup, you should consider using a mixed potential scheme like the virtual crystal approximation (VCA) or if you are interested in just the electronic structure KKR-CPA calculations can be very effective. You should look into the drawbacks of these methods versus a supercell calculation, however. This includes the inability to represent local structural distortions at the dopant site.
I think you can make super-cell of 2x2x1 or of any size, but make sure, this size of super-cell contains the cubic symmetry of unit cell. i mean in all planes the cubic symmetry must be maintain in supercell.
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