That is only a part of the schematic.
I gave a link to the schematic of the Adafruit SD module with the HC4050. It shows that the inputs of unused port are connected to ground.
There has to be only one 3.3V MOSI and one 3.3V SCK signal. The CS for the SD memory card is of course not the same as the CS for the Flash.
So these are the signals that needs to be converted to 3.3V: MOSI, SCK, Flash, SD.
That is only 4 signals. A HC4050 has 6 ports.