In order for me to see where disk space is being used up (regardless if it's in a mysql table or not), I use my trusty "du" command. Here's an example of me finding where all the space is being eaten up from.
$ sudo du -cks /* | sort -rn
You can see that the majority of the space is being used by this folder.
That folder holds data tables. In order to see which tables are taking all the space you can proceed like this using the "human" or "-h" option. I like to do disk space management this way because sometimes you cannot even log into mysql because you don't know the password or user.
$ sudo du -chs /mysql/*
You can see that all space is being hogged by a few tables holding many GiG's of data. Hope this helps.