My buns both thump, what seems to me, randomly. I'm sure they hear or smell something I can't. Rabbits are overly sensitive to the most minuscule changes, noises, smells. It's how they can anticipate danger in the wild.
Mine have no problems with the vacuum, the airplanes flying over, the motorcycles, or the noisy air conditioner. But occasionally they will "freak out", thumping and acting skittish to some perceived threat. I think the key here is "perceived". There might be nothing, but Arlo just has a "hunch".
Or my house is haunted. I assume rabbits can see ghosts, like cats can.
They also thump to show disapproval, but this thump is while seated and staring at me (or the other rabbit, whichever is needing disapproval), rather than alert, ears up, and skittering around.
Occasionally, they thump for attention. Lucas will come into a room and thump to announce his arrival, and to make sure I'm paying attention to him!
Excessive thumping can be stressful for the bun, though, depending on the cause, so I always make sure to comfort them (or distract them with a treat) if they look to be thumping on alert.
Rabbits are super-easy to understand!