Yes, the pro or anti-squat forces do come into play, but on most sports bikes the are designed to cancel themselves out to a large extent by an appropriate swinging arm pivot location. The maximum contribution of additional load on the rear suspension due to squat forces are roughly 10%.
If you really want to confuse yourself, have a read of this book:
Motorcycle Handling and Chassis Design. I've made extensive use of his design analysis software in my own bike project. Seems to work alright.
