I just wanted to say that that is one reason the files are delayed, everyone is free to apply but the results will all be delayed till the time the situation is better. I understand and acknowledge the fact that there would be a lot of spouse's whose study or work permits will expire soon due to this delay but this is just unfortunate as no one expected the restrictions to extend this long. Also, IRCC does give you an option to apply for a study permit and spouse visa together, however, most people and consultants prefer to do it separately for the fear of one being affected by the other thus fear of rejection and when you apply separately, there can be unexpected problems like this.
The fact remains that even if the student visa or their work permit is going to expire if the primary applicant does qualify for PR they can still call their spouses later on OWP so again there is no rush. The debate can go on and on, but the fact remains, whatsoever may be the reason for the delay, there is nothing much one can do apart from wait and hope the permit is approved in time.