XenForo has never uninstalled an add-ons files, that's something you have always had to do yourself.
In XenForo 1.x to install an add-on you had to upload the files first, then in the ACP you had to upload an xml file. XenForo had no idea that an add-on was ready to install prior to this. When you uninstalled, it removed database entries etc but didn't remove the files. So technically the add-on was still there ready to be installed again if you wanted to but XenForo did not know this.
In Xenforo 2.0 to install an add-on you have to upload the files first. However XF 2 is more 'intelligent' and now knows that there's an add-on ready to install. Just click install to do so, no need to upload anything into the ACP this time. So when you uninstall, the add-on shows that it is available to install (which is is). It also serves as a nice reminder to remove the files from your system if you really no longer want it.
It would be nice to have full capability to install and uninstall everything from the ACP. Maybe this will come in a future release of XenForo 2.x. For now, we do have an improvement on what we had in XenForo 1.x