Back in the day....
when suspension forks were young and seal technology not so good, they were necessary. A properly designed rubber boot DID keep crud out and off of the seals. However it was still a requirement to lift them and clean under them after just about every ride. They didn't accelerate wear, at least not the ones with the accordian fold. They only touched the stanchions in one spot, at the top of the boot. The lower part of the boot had a lip that fit into a grove in the top of the lowers. They worked okay and did help fork and seal longevity. To be quite frank most of the arguments against them were pretty much ******** at the time. However as forks came out of the "toy" stage and manufacturers got serious and started using good quality wipers and seals, the boots became nothing more than an unnecessary expense and were dropped. There was a lot of hold over and lag in getting rid of them, and not all forks got the "good seal" treatment right away. But eventually even the lower end stuff ended up not needing them.
As for other types of fork boots, like the Lizard skin, those are detrimental to the fork stanchions, they trap water and hold grunge against the stanchions and tend to wear them faster. They also tend to bunch up and effectively reduce the travel of the fork in the last part of the stroke. All the complaints that were piled onto the old rubber accordian boot are quite valid when it comes to the tight fitting neoprene type boot.
Anyway, that's what happened to the old rubber fork boot. They became obsolete and unnecessary.
Good Dirt