2D convolution is already very highly optimized in the functions conv2() and imfilter(), even more so for separable kernels. I know for a fact that they put special effort into making these as fast and efficient as possible.
Convolution via fft2 may not be faster, especially for smaller matrices like you have. In fact it might even be slower. Generally the fft method becomes faster only for very large matrices. You can test that by increasing the size of your matrices.
