PaulRB:
So on interrupt, the Arduino performs 2 read and 1 write operation, @400MHz, albeit 16 bits each.
I'm afraid that speed is a tad optimistic 
Mivae:
Also visual feedback for the parameters isn't absolutely necessary. If I were to use potentiometers I could neither address several synths at once nor store patches because values would always have to be absolute, and that's just not practical I'm afraid.
The interrupts can come in very useful here. You can basically be writing your outputs constantly based on the status of all your encoders, even if it takes 1-2 ms that's no problem. Whenever there's an input available the interrupt will ensure it gets handled there and then.
Which starts me to wonder: will you have enough memory to store all those values? Arduino's working memory is rather limited and you will have to keep them all in RAM.