All of the service classes in Lemoon make heavy use of the cache to improve performance and reduce roundtrips to the database. As an example, almost all methods calls in the ContentService will return data from the internal cache instead of the database.
When the clear cache function is called, all objects in the internal cache will be removed and subsequent calls to methods in the service classes will hit the database.
Note that the clear cache method only removes items put in the cache by lemoon, any items placed in the cache by your custom code will not be removed (this is why the items in cache count almsot never reaches 0 even after the cache is cleared).