You're right. Atlantic mackerel doesn't have an acoustic survey, but given its biology, it's not the best species to consider with acoustics. It doesn't have a swim bladder, so it's not a good acoustic target.
However, the department runs an egg survey. They monitor the number of eggs spawned during the short spawning season in the southern Gulf of St. Lawrence. As you mentioned, the spawning can vary a bit from one year to another, depending on the temperature. The survey doesn't vary in time, but there is sampling of the females, as well, to account for and correct the mismatch. I know that the department has explored other potential spawning areas, like the west coast of Newfoundland and Nova Scotia.
In my view, the survey for the Atlantic mackerel biomass is a good one, compared to many other forage fish stocks. There is uncertainty, but when I read the stock assessment reports, I very much trust the conclusions about its abundance and the fact that the adult mortality component is too high right now.