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In costFunction(theta, X, y) we don't need to transpose the array theta. In fact ,the implementation with theta.T in the sigmoid function works because in this case theta.T = theta . You can test it by print(theta , theta.T) which prints [0. 0. 0.] [0. 0. 0.]. In case we cas see the true transposition of theta with print(theta , theta[:, None]) which prints [0. 0. 0.]
[[0.]
[0.]
[0.]]. In this case the code would't run , so theta should not be transposed.