Choosing a two-bladed propeller will indeed make the aircraft have a faster cruise speed like you say (due to less drag). Whether a propeller is chosen to be two- or three-bladed depends on the performance the designer/manufacturer wants to achieve. If you want to compromise cruise performance for extra take-off and climb performance you would rather have a three bladed prop.
I don't know any specific details regarding the PA-31, but I guess the reasoning might be as simple as that extra take-off and climb performance was preferred rather than a few knots extra cruise speed?
I am not sure how this affects Vmca, but if I were to give an answer I think since three blades gives more drag, Vmca would be higher (higher speed needed to have sufficient control-authority to overcome yawing moment). Also, since having more blades will increase power absorption from the engine at low speeds, this should also increase the yawing moment causing Vmca to increase.