As I have suggested and explained elsewhere, I doubt the hold up (for most applicants) is really the clearance. Odds are good that necessary clearances have been submitted and the application is in queue for a processing agent or Citizenship Officer to take the next step.
Compare: the courier records the application delivered to CPC-Sydney on a specific date, and the applicant calls the help centre within the next few weeks or even a couple months, and so far as the call centre agent can see, there is nothing to show the application is in CPC-Sydney. But it is there. It is there waiting for a processing agent to open the file and conduct the completeness check.
My strong impression is that there is a similar scenario regarding clearances. They are there. But the file is waiting for a processing agent or Officer to access it for the purpose of taking the next step in processing it. Including reviewing whatever the clearances reveal (nothing at all for the vast majority of applicants; no arrests, no convictions, no pending investigations, no prohibitions for Removal proceedings, and so on).
There are also some hints "waiting on . . . clearance" has also been employed as a stock brush-off response, a way to quickly get the applicant off the phone.
Sure, there are occasions when applicants are held up by clearances . . . especially security clearances relative to which CSIS has concerns. Almost any applicant at risk for this will have a good idea of his or her risk. These clearances can delay applications for YEARS. I have seen reports of actual cases in OFFICIAL sources where citizenship applications have been help up by clearances for as long as EIGHT years.
And, on some occasions it is possible that the call centre conversation is taking place during a window in time where there is indeed a referral for a clearance not yet submitted by RCMP or CSIS . . . but for the vast, vast majority of applicants, among whom referrals for clearance or updates of clearances are done in batches of up to 100 applicants per request, the clearances are done and it is more likely the local office person responsible for the next step simply has not yet gotten to the file in his or her queue.
Remember, except for the unusual case, it is not as if there is any gumshoeing involved: there are some structured electronic queries made into multiple digital databases, most of the relevant databases accessed through a single query. No hits, clearance done. For the vast majority it is that simple: no hits no problems no delays. Call centre agent weak excuses aside. (In their defense it is obvious they are besieged with unnecessary are-we-there-yet inquires while they too are well aware of scores of clients with important questions having difficulty getting through on phone lines clogged with an inordinate volume of frivolous calls.)