First, crew from deactivated ships is already handled; their average skill points are checked, compared to the racial skill point rating for the Academies and if higher, tossed into the crew pool, and if lower the fraction difference is tossed into the crew pool. IIRC anyway.
The biggest issues with mothballing is how long it takes to take the ships out of the mothballs, what facilities you'd use, what parts need to be replaced and how much it costs while in mothballs.
But I don't want the crews added to the pool, I want them added directly to new ships that are built to increase their starting grades. Or to old ships, to strengthen your peace fleet during the mass mothballs that might follow a war's end. I want the grade bonus of the old ship's crew to be preserved rather than converted into more or less manpower.
You always could just dump them into the pool, though. Don't see why that shouldn't still be an option anyway.
How long it takes and the cost would be simple enough. Just the time, facilities, and MSP necessary for a full overhaul from 0-100% on the ship's maintenance clock. Maybe more time than that, it really depends on what "balance testing" says after we get our hands on the game, but I think that's a good enough initial baseline. It wouldn't require any different facilities to those required in normal maintenance and overhauls imo. There's no reason to make more parts of the game for it, it could just be part of the normal maintenance mechanics.
The resources they'd consume in mothballs is tricky, but you could just throw an arbitrary number out and just tweak it as we play the game more and decide what seems fair. For my own arbitrary number I'd say either 1% of the regular MSP for maintenance, or 0%.
No parts would need to be replaced, it'd just be the old ship at full readiness. For missile boats and carriers that'd probably end up being just fine. For melee beam brawlers it would probably be a little more questionable as far as how worthwhile they are to keep in reserve, at least if they become obsolete during that time. iirc most of the ships pulled out of reserve in the Starfire novel "Crusade" were light/escort carriers anyway.