I don't know about that. The profit is in game sales, and you can't play games without controllers. At launch, the cost of just the parts of a Joy-Con (to assemblers) cost more than the price of a Joy-Con Pair at market prices. Sure Nintendo probably got some discounts for them, but the Joy-Con are packed with technology. The profit margins at launch were extremely slim, if they existed at all.
Now there's been time to refine the design and let old parts get cheaper, I'd say there's a good chance they'd consider superior sticks. However if they DO move to hall-effect sticks in the next Switch, I doubt they'll announce it. That would essentially lose them every lawsuit on the matter instantly, since it would admit fault. If they do it silently and market them as "no deadzone" or "more accurate" analogue sticks, maybe they'd get away with it. My expectation is that they simply won't fix it, and if they do, they'll remain silent on the matter for legal reasons.