No just upgrade Aperture once you have installed Mountain Lion. Also if your version of Aperture did not come from the Mac App Store you will need the serial number(s) when you install Aperture after the upgrade to ML. Make sure you have them. If your current 3 is an upgrade you will need the original serial numbers also.
If you bought from the MAS then that will not be an issue.
If you do an overlay install (just upgrade the OS) and not a clean install (wiping the HD and starting from scratch) your data files SHOULD not be touched. However it is important that you back up the disk before doing the install in either case. Things can go wrong.
I suggest you get an external drive at least as large as the internal and clone the internal to the external. This way you'll not only have a backup if something goes really wrong you can boot off the clone and restore your system back to what it is.
And again make sure you have the Aperture serial number before you start. Doing the install as an overlay, you shouldn't be required to enter the serial number but it's good to have just in case.
Post back if you have any other questions.