There are surely other, more complicated reasons behind why they are only able to run limited trains on certain rides. For example, they may not have enough staff to legally/properly operate at full capacity on every ride during this time. There's also the issue of certain trains being broken, as I've witnessed the sensors go foul on several PK trains, causing huge delays. Then there's maintainence and inspection issues, such as a train or arm needing to be inspected by a state or certified inspector before being put back into operation... The list goes on I'm sure.
As far as Taffy goes, I've seen them making it a lot during the Christmas season, but I never go in there any other time.