From what little I know, if Trunk port is configured for additionally for Q-in-Q, storm-control can NOT be applied.
As for using it on Trunk ports, it is probably better applied further out in the network at Access layer (I assume Trunk = Core), but if Core is dual Active-Active, it is just one additional feature/function that may help your network stay up under certain unknown conditions.
I would not recommend only setting at Core. Set at edge, and then potentially core. You need to decide if taking down such a Core port to potentially save others is acceptable. This also assume you are setting Storm-Control active to block.