Every site that is built has an impact. You can't go more than a 2 or 3 hours without coming to another site on any of the trails that I recall. Many are 45 minutes apart. I wouldn't want to see any more sites built.
Thru hiking by GSMNP definition means one that has started 50 miles or more outside of the Park and ends 50 miles or more beyond the Park. The original conceived notion was derived from the fact that a day, or up to week of hiking, was physically deteriorating to the human body, but good for the sole (re-creation of the sole). Back in the day, when this idea first came about, the work force was substantially involved in physical efforts, not desk jobs. For years, there was a common belief that hard physical work shortened the life span. There was no high tech backpacking equipment or freeze dried foods. Long distance hiking became attractive when trail sections were joined together. Even where there was no trail, blazes were painted on the roads to connect sections. There was obviously some intent to make provision for long distance hiking, even though at the time, it was not generally thought that someone would hike end to end. Today we have thousands doing it, so it has become somewhat mainstream. You have many people in the workforce that use their entire vacation to do nothing but hike the AT and a lot of teachers and seasonal workers do attempt to thru-hike. I do agree that any long distance hiker should carry their own shelter, which, to me, means they already paid their way. To charge a 2nd time for use of a shelter or a spot outside the shelter is just not right. I just get the feeling that your money is going to subsidize something else and this does create a hardship on thru-hikers. There is nothing these people get in return for their fee. The trails are maintained by volunteers and true thru hikers generally subscribe to LNT. They are in and out of the Park in just a week to 10 days.The AT was originally conceived to provide a trail that was within a day's drive of major industrial centers in the eastern US so that working people could use it to recreate. Thru-hiking was not considered a typical use and was considered by many a stunt even 20 years later or so when Earl first did it. Thru-hikers have no more right to trailside shelters than do any other hiker. And all thru-hikers should be carrying suitable tent or tarp should a shelter be full when they arrive. As to creating "additional hardships on thru-hikers" - I think that falls on many deaf ears. Not many folks are going to pity a person who can take a 6 month vacation.