Back in the mid 90s, a retired weapons tech who lived in the area related to me that he had been tasked with tearing down sniper rifles back in the 60s while working at 202 depot. The rifles were still in their chests, but the scopes had all been removed by that point. One still had the scope, which he reported to his Sgt. The Sgt merely said: "there are no scopes". So he retained the scope and brackets (I can't remember if it was a 69 or a 32TP) and built up a sniper using an unserialised receiver to which he added his SIN number as a serial. I had seen that rifle with his son.
So the answer to some of the missing Canadian rifles could be as simple as they were destroyed by the CF upon disposal.
There were a couple languishing in the depots around the year 2000. I talked with the retired Life Cycle Manager, who made the decision to give them to the Rangers to use rather than see them destroyed. They could have been put up for distribution to CF museums, and if they survive their time with the Rangers, may eventually be.
Here is a shot of a serial number from one of two chests I found at a surplus yard about a decade back. The owner of the yard could not recall when he got them, and they were mixed in with dozens of regular Cno7 chests. Most likely that rifle ended up in the smelter.