How about adding an optional argument "scaled", defaulting to True:
Then if S is an S-box, for instance
sage: from sage.crypto.sbox import SBox
sage: S = SBox(7,6,0,4,2,5,1,3)
one could call
sage: S.linear_approximation_matrix()
or
sage: S.linear_approximation_matrix(scaled=True)
to get the scaled matrix, and
sage: S.linear_approximation_matrix(scaled=False)
to get the unscaled matrix.
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