The effect of Interrupt from motor encoder reading

Hello,

I will be using 4 DC motors with encoders attached to my Arduino Due. They all use dual channel Hall effect encoders? I am using them to provide feedback on the motors' actual speed. I understand that the use of interrupt Service Routine will affect the accuracy of millis(), but I have been using millis() in other time-sensitive functions at the range of 100Hz.

Will the use of ISP affect the accuracy of the other time-sensitive functions? If yes, are there any alternatives that I can use to count time? Basically I am using millis() to make sure that my fusion sensor algorithm and PID functions are called at a fixed intervals.

A little timing jitter should not be a big problem at 100Hz.

Nick Gammon wrote a very interesting page about interrupts and timing : Gammon Forum : Electronics : Microprocessors : Interrupts
You can read on that page that an external interrupt takes about 5 µs plus your own code.
Keep the code very small, for example only increment an integer, and do everything else outside the interrupt routine.