I make today some test.
First, i use PinChangeInterrupt library to configure an single pin (A0). In handler function i put an simple incremental instruction.
Motor have limit switches so I left to go through the whole interval on both directions.
I found aprox. 20.700 pulses for about 58s of working time. I got same value with small variations (few counts) because switches don't close at exact same moment. Also i got same number of pulses in both directions.
Second test i use my implementation for pin change interrupt witch is an simplification of what is in library. I got same number of pulses in both directions.
Third test: now i use my implementation for pin change interrupt to count pulses for both motors working simultaneously. I obtained same number of pulses like in previously cases.
So, in conclusion, i don't see any difference between using simple incremental in ISR routine and something more complex like increment or decrement two counters with some conditional inside.
Later i will make another test, but this time i will use one external interrupt to see if got some differences.
@Robin2: so i have about 340 pulses/s. I don't know if these correspond to real number of rotation because inside are some gears, but i don't think that is very important at this moment. More important is how many pulses come into one second.