Hey there, if your version of PinballX is really old (like, pre-.NET), the installation might see it as a new install (different app GUID) and overwrite some of your stuff. Just to be safe, back up your pinballx.ini and database directory before you install the new version.
Yes, you can install straight over the top. No changes will be made to media files or config (except maybe adding some new options, depending on how old the version is you're updating from)