there are huge benefits to doing things barefoot. It really strengthens the fascia of your foot. We wear shoes to much and usually are underdevelope in that area. Thats why we see so many plantar fasciatis injuries. If you look at kenyan runners who are always barefoot they never suffer these injuries.
I wouldnt start squatting real heavy barefoot, might be a bit much. Infact i would suggest going barefoot during a dynamic warmup then shoes and then just keek progressing towards shoeless squats. last thing you want to do is suffer a foot injury. It will put a halt to all of your training immediately. Good luck and always think on the cautious side when trying a new style of training. Ease your way into it.