48 inputs and 48 ouputs with arduino mega

-Rotary encoders to digital pins 21-53.

21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50,
51, 52, 53

33 pins for 16 encoders?

Encoders are usually read using interrupts. The Mega does not have 32 external interrupt pins.

Is there going to be problems with latency

Most likely, along with missed encoder changes.