numpy.savetxt() outputs very large files
The size of the native datatype differs from the size of the string representation of the datatype.
numpy.savetxt has a fmt argument that defaults to '%.18e', which formats each of your zeros as 0.000000000000000000e+00. That is 24 characters per item plus one for the delimiter.
To get a smaller file you can change the format (beware of losing significant digits) or use numpy.save to save in binary or numpy.savez to save as a compressed archive.