Unless MySQL changed it since I last looked, the one large innodb file is a big PITA, but otherwise you can do OPTIMIZE TABLE to compact tables; apparently this can sometimes be done in place, but I'm used to it writing to a new file so you'd need room for old and new; and at least for MyISAM locks the table for the whole time, so I hope you've got a way to manage that too, but that's about the same as VACUUM FULL.