The coefficients of the discrete fourier transform of FCC are all the same, may be taken equal to 1, whereas the coefficients of the HCP fourier transform are not all the same. That is because FCC is a lattice, but the HCP packing is not a lattice.
In other words, because FCC is a lattice the structure factors of FCC are trivially all equal to one another, whereas HCP has nontrivial structure factors that will appear in the coefficients of your fourier transform.
If you plot |FT(FCC)|^2, you should see peaks of uniform height. If you plot |FT(diamond)|^2, you should see peaks with heights in ratio 1:2. If you plot |FT(HCP)|^2, according to https://en.wikipedia.org/wiki/Structure_factor#Hexagonal_close-packed_(HCP), you should see peaks with heights in ratio 4:3:1.
A lattice or packing may be represented by a distribution of dirac delta functions with equal coefficients. A lattice has one of the delta functions located at the origin. The fourier transform of a lattice is a lattice, called the reciprocal lattice.
FCC is a lattice and its reciprocal lattice is BCC. The fourier transform of FCC is the BCC lattice.
A general regular non-lattice packing like diamond cubic or HCP will usually be a sum of N lattices that are offset from one another. For instance, diamond cubic is the sum of two offset FCC lattices, so its fourier transform is the BCC lattice times structure factors. I think that HCP is the sum of two offset (A2 x Z1) lattices.
In general, the fourier transform of such a regular non-lattice packing that is a sum of N offset lattices will be the reciprocal lattice times phase factors, "structure factors" per wikipedia. You can see a discussion of diamond cubic https://en.wikipedia.org/wiki/Structure_factor#Diamond_crystal_structure. They define the structure factors to be complex, (1+(-i)^(h+k+l)), but if you use symmetric offsets of +/-(1/8,1/8,1/8) instead, that allows the structure factors of diamond cubic to be real-valued, 2 cos(pi/2*(h+k+l)).
Regardless, the absolute values squared of the diamond cubic structure factors, which correspond to nodes of the BCC lattice, occur in ratio 0:1:2; and those of HCP, which correspond to nodes of A2xZ1, occur in ratio 0:1:3:4. Again, you should see this ratio 1:3:4 when you plot the peaks of |FT(HCP)|^2, whereas the peaks of |FT(FCC)|^2 should all be the same height.