Very possible and the bungee/rubber band trick should help if this was the cause.
Set them to minimum - if you haven't tried this already - just to see if they are a contributing factor.
I've found blu tak to be really useful to minimise vibration. Same with hi fi stuff
No. It could be the HDD but it could also be one of the fans. Even the PSU fan. Just put a rubber mat underneath.
Do be aware that by putting your PC on a glass table you are effectively making a speaker. You need some sort of noise dampening if you are going to continue to use the HDD with the PC on that table. Or you could replace the HDD with a SSD or NVME drive.