I can't talk about the details on Citrix servers. However, with ClickOnce you cannot tell where the application is installed. It is installed under the user profile, no ifs, ands or buts. One of the main goals with ClickOnce was to improve security and install applications in a profile, which became easier. So, if you clear the profile, you are stuck.
However, were you unable to simply deploy the application to the Citrix server without ClickOnce? Most .Net applications can simply be deployed to xcopy, so it would be fairly easy to write a few batch files to copy the latest deployment to your Citrix server and skip ClickOnce together.
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