In the past few years, a few specific studies have caught my eye. The first was a Japanese study which showed 80% of tendon cells in a petri dish at 48 degrees Celsius (118.4 degrees Fahrenheit) were killed in just 10 minutes. It's entirely common for horses' legs inside boots to reach that temperature or higher, especially during the hotter summer months. The second study ties directly into that - recent research from the University of Veterinary Medicine in Vienna showed wrapped or booted legs can increase skin temperature by over 30%. There was another study a few years ago that I haven't been able to relocate (if anyone knows what I'm referring to, please send it to me!) which gave some specific temperatures of horses' legs inside neoprene boots. They were routinely well above 100 degrees. (There's some information on that here, as well). A bare-legged horse's tendons reach 113 degrees when galloping, according to Dr. David Marlin.
That all being said, I completely understand and support using boots when they're clearly needed; for instance, in situations like with SnowPony or for going cross-country. Where I start to hesitate is for regular everyday riding, mainly on the flat. This specific concern stems directly from my history with suspensory injuries. To me, the idea that I could be doing something that contributes to tendon cell death and injuring my horse, is terrifying.
I ride Lucy bare legged most of the time, thanks to her history of suspensory injury, although it bears noting she hasn't been in full work in a few years. As mentioned before, SnowPony goes in all of his 'gear' because he's not a straight mover. This fall, I rode in Equifits and liked them just fine. Last summer, I rode Lane in a pair of simple galloping boots because as he was learning to carry himself as a non-racehorse, he would occasionally trip over himself. They weren't my favorite, but were what was available and protection won out in that instance. Lastly, the working cow horses and reiners I've been on all go in SMBs, and for good reason - when they're digging down into the dirt so low, they're much more prone to clip a fetlock and need the full protection.
I don't think it's a simple black and white decision to make, to use boots or not. There's so many factors that play into it - horse's history, geographic location, discipline, and personal preference. I don't have a 'right' answer, but I'm interested to see other opinions and experiences.