It seems to me that if the store doesn't take stored smithore into consideration when it sets its smithore price, it should also not take stored food and energy into consideration when setting those prices. So if someone has a large stockpile of energy and someone else has an energy shortage, the store should jack up the energy price very high to encourage the stockpiling player to sell.
The thing you need to remember here is that Food and Energy have the players as end-consumers, in a sense. They're the ones who ultimately decide how much those are worth to their purposes.
Smithore, OTOH, is a slightly different story, as the Store uses it to make MULEs (which, in turn, get sold back to the players). In a sell-off situation, the price of Smithore will be exactly what the sell-off price was (average per unit sold), which means that MULEs will be double that next round.
In other words, they aren't profiting off this at all; they're just selling your Smithore back to you in 2-unit chunks that can actually do useful things.
I wonder what would happen if there was an inherent labor cost applied to the price of MULEs, making them worth much more than the Smithore the Store bought to make them? At some point, this would make Smithore shortages more paralyzing than lucrative, as no one would want to install expensive MULEs with the burden of having to produce enough stuff to make back their debt (already, I've played games where I simply didn't bother buying MULEs until the price went back down, figuring that's why I ensured I ate enough Food to have the time to do double-or-triple-duty on MULE installing in a later, cheap-MULE turn.
The game must assume the Store has unlimited cash with which to buy everyone's stuff, or there wouldn't be the thrashing that's going on (the Store can't buy your Smithore for $260 because it's broke???) You're mining resources, creating value out of nothing (or at least a very advantageous exchange rate for the Food you ate to have time to install the MULE, and the Energy you used to power the MULE, to "create" the Smithore/Crystite).
I would be curious in having a mode which tracked what money position the Store is at throughout the game. It might help people understand the Store's role, and if future versions/improvements can enhance the economic model in a way that is both interesting, realistic, and fun.
Or maybe the Store would place a limit on the number of Smithore units it would buy - say, some amount relative to the amount it needs to have a full Corral?