Firstly, the most important thing to remember is that only the Information Store backups can be used for disaster recovery.
Basically when you backup the Information Store you are backing up the entire of Exchange, eg you have all the content, the structure, and settings etc, which would allow you to do a complete disaster recovery restore of your server (in conjuction with the system state and install files obviously) if you needed to do so.
The mailbox / public folder backups is basically a kludged work around to allow you to restore individual mail items, rather than having to restore the entire of Exchange as one (and therefore overwritting anything which has since happened). It works by using Outlook on the media server to connect to Exchange as each individual user, it then reads through every mailbox item within that users mailbox, and backs up the information, before moving on to the next user and repeating the process. One of the big downsides of this is that you don't get the advantage of things like single instance storage for the e-mails (though I think you do from v10 onwards), so if you sent a 100MB file to 9 people on your network, it would take up 100MB on Exchange, but 1GB in mailbox backup storage.
So if you have the time and storage available then it may be worth continuing to have both, but if you had to decide between the two then you should always ensure you have the Information Store backed up.
