server certificate has nothing to do with the CODE SIGNING certificate you used for your clickonce application. So you are correct - users who will open webpage to download the installer will see "invalid certificate" message from the browser. But after they download the app, it will install just fine.
Please note - i assume you used timestamp server when you were signing your clickonce app. Otherwise, your signed clickonce app will expire when your code signing certificate expires. But again - that's a side note and it has nothing to do with the web server certificate.