A) mach doesn't do encoders.. see note 1
2) Your pulse rate depends on the computer. I was getting 50k base threads on a 600mhz pentium 3 - IIRC that was pushing it. (the computer gets sluggish the faster you try to push it.) This means - either you could run steppers at 25khz (base thread/2) or you could read encoders at near the base thread speed (near 50k)
now if you get external hardware - you could count encoders much much faster than that.
you can look at my thread where I started looking at using just the printer port to run servos. - it is very doable.
Large Brushed servo setup on the cheap (WIP)
The real question is - do you mean 'encoder' or 'stepper'.. Or maybe 'what are you trying to do'
Note 1. mach needs external hardware like geckos to run servos. Mach is really a step and direction program. (This is a broad statement - others should expand on it as I have no experience with it)