A well designed and installed fork boot really helps to keep dirt and grime out of fork internals. Ironicly, most factory installed fork boots either have vent holes or fit poorly, making them useless. Also, around the mid '90s, pro racers (who got free parts and had an army of mechanics to service their ride) tended not to run them, giving amateur riders a good reason to remove them out of hero worship.
Fast forward to today - most high end forks don't come with boots. The fork manufacturers assume the owner will maintain them to 'race' standards: clean the exposed stanchion tubes before and after every ride, oil changes every 25 hours and a compete overhaul after every 100 hours.