When one is working with complex matrices, "transpose" very nearly always means *Hermitian* transpose, that is, A[i,j] <- Conj(A[j,i]). One often writes A^* for the Hermitian transpose.
I believe that I have actually (many years ago) used a true complex transpose, but I agree that one more often needs the conjugate transpose. I would not be in favour of changing t() because I feel transpose means transpose -- certainly where there are non-square matrices. But I'd be in favour of adding a conjt() (or some similar function) that does the conjugate transpose efficiently. JN