onSessionEnd not working properly

I suspect that you need to change how you are referring the session and application scopes.  From the CF documentation: "Use the SessionScope parameter  to access the Session scope. You cannot reference the Session scope directly; for example, use Arguments.SessionScope.myVariable, not Session.myVariable.  You must use the ApplicationScope parameter to access the Application scope. You cannot reference the Application scope directly; for example, use Arguments.ApplicationScope.myVariable, not Application.myVariable."

http://help.adobe.com/en_US/ColdFusion/9.0/CFMLRef/WSc3ff6d0ea77859461172e0811cbec22c24-7d40.html

Try this (code not tested):

<cffunction name="onSessionEnd" returnType="void" output="false">
    <cfargument name = "SessionScope" required=true/>
    <cfargument name = "AppScope" required=true/>

    <cfquery name="deleteCartRows" datasource=#arguments.AppScope.datasource#>

          DELETE from webCart

          WHERE unique_session_ref = "#arguments.SessionScope.unique_session_ref#"

    </cfquery>

</cffunction>

You may also want to use CFQUERYPARAM within your CFQUERY, this is unrelated to your session issue.

CFQUERYPARAM:

http://help.adobe.com/en_US/ColdFusion/9.0/CFMLRef/WSc3ff6d0ea77859461172e0811cbec22c24-7f6f.html

I should add, what's actually going wrong is that the rows in the webCart table aren't being deleted when the session ends