Ren, you're quite right in that sense. When starting from fresh, the used, stored saltwater would be fine. As its only live rock in the setup's most of the time, the potential ammonia contained in the water isn't a problem, as it will eventually be broken down into nitrates by the bacteria in the live rock.
The problem is when you have an established tank with corals and livestock. Doing a water change that is designed to kick nitrates and replenish trace elements and replacing it with water than may contain ammonia, nitrites and nitrates, could potentially kill your livestock. This is what Jtnova is considering doing, to save money on salt and ro water. This is why I suggest that he tests the water in the individual buckets before adding it to the 12G nano, if he does decide to try re-using the water from his 90G.
Any nitrites, nitrates and phosphates that are in the water from the 90G will remain. Any dissolved or undissolved organic matter that is in the water from the 90G may break down into ammonia in the buckets and remain as ammonia.