I have experienced thumping for a variety of reasons and it is frustrating when you have no clue what caused it.
When my buck was caged he would thump if it was his usual time to come out and I didn’t let him out. It could be that he is expressing his displeasure of not getting attention exactly when he feels he deserves it. I would find it odd that he did this when he was in the middle of sleeping though.
I also had a buck that woke me up at 5:30am thumping in his litter box that had a metal grate. I went to calm him down and he still sat in his box and continued to thump. That was fun! I am guessing there was one of three things that could have caused my buck to do this. It was either a sound, something out the sliding glass door that scared him or something that was on the floor outside of his pen that wasn’t there before.
If your buck woke up all of a sudden and did this I would say it was probably something he had seen or heard.