There are 3 different PSoC families and they all behave differently. The Mux is not the problem as long as you do not use one that needs a clock. From deep sleep mode on, all components using a high frequency clock (derived from the system clock) are freezed.
The GPIO are maintained in PSoC5, but in PSoC4 the IOs are frozen in hibernate mode which will probably give trouble with your connected mux.
So you may use deep-sleep mode freely, but give it a try.