yes, all the bots use the same db. there are a few tables that do not have a bot prefix: online, alts, etc. By having only a single db, this info is shared by all the bots. I am currently running 10 from a single instance of the db, and other than a few little nuances that also plague the ones that only run one instance, have had no problems.
If you are running multiple bots it would be wise to check out:
http://bebot.link/wiki/multiple_bots as this will explain things a little better. Basically you have on bot.conf per bot, and only one mysql.conf. This does make it easier, as if you update a module, you only have to replace one file, instead of multiple file scattered throughout your bots.