I believe it just uses file names and paths, so if all that is happening is the app is getting updated, you should be OK in my experience. OTOH, I've seen some cases of apps that, upon running the first time, create or dump a whole bunch of extra files and folders on disk (see Office for a perfect example) and the Uninstall process will not see these extra files and folders since they aren't part of the original installation. So in some cases, you can get left with remnants of the application's support files.
Again, for simple drag and drop apps, it should be OK. but for more complex apps/installs, you'd be better off looking at a custom uninstall script.
I've had really good experiences uninstalling .dmg's created with Composer. The index seems to use the filename and path mm2270 mentions.
I also have a personal policy to making sure that I keep older packages around just for those situations where an update has dramatically changed locations of files. Generally these are major rev packages. Something like Firefox or Skype will probably never give you an issue if you plan on leaving your users settings alone during an uninstall.
Thanks for the help, just wanted to make sure.