Generally, instructions that operate on registers take one cycle, instructions that operate on memory take two cycles, and "special" instructions take 3 cycles. This is highly simplified -- you really want to look at the data sheet -- but this is a good first-order approximation for estimation purposes.
And, yes, with a 16 MHz clock, one cycle is 1/16000000 of a second 
However, for driving external hardware (steppers, servos), then you should either use an existing library, or use the timer/counter/PWM functions built into the chip, rather than try to emulate the same function in software.