There's really no difference. A reboot just saves you from having to shut the computer down especially if you are doing software installs and want to get right back to the desktop. When you reboot the computer it shuts down processes that are using up needed memory and kinda refreshes the computer. This is why a reboot is necessary as a problem solver when you are having issues.
I don't know what method you used to remove iTunes but it might be better for you to use App Zapper or App Delete to get rid of all of the iTunes preferences. After that then you can reinstall iTunes from Apple's website.
Here's a link to App Zapper. If you've already emptied the Trash then you will need to reinstall iTunes and then remove it again with App Zapper.
http://www.versiontracker.com/dyn/moreinfo/macosx/28764