For some applications this is a very useful technique to assure, the user runs the latest version.
For some applications, you may experience difficulty with settings files. Settings files in that way, that users store local data in there, and that these changes are not going to be lost on the next app-update.
There are 3 known circumstances, where your settings files will not get updated:
1) downgrade your deployment version (e.g previous version was 2.5, new version is 2.3)
2) change your deployment provider url
3) changes in public key token/certificates
So if you can make sure, that none of the 3 reasons will ever appear, let click-once setup handle your settings files.
Otherwise, you might consider moving the files to a location outside the click-once environment (e.g. the localappdata folder).
Get an idea of how to do this in this article.