Are Clustered Index Usage Stats skewed since they are referenced in Non-Clustered Keys?
The user_lookups column of sys.dm_db_index_usage_stats is a count of clustered index key lookups (a.k.a. bookmark lookups). This indicates a data row retrieved via a non-clustered index using the clustered index key row locator. The separate user_seeks and user_scans columns for a clustered index count the number of times the CI was used directly. 

These columns allow you to determine how the clustered index is being used in query plans.