Are you sure "Darkness on Ilum" gives you more Daily commendations for doing the bonus? I haven't heard that mentioned anywhere. There aren't any Imperial dailies that give you extra Daily comms, AFAIK. The bonus for "Poisonous Shipment" (Ilum) only gives you a few Legacy XP (not worth it IMO).
Just Personally confirmed that there is a bonus mission for "Poisonous Strategy" that also gives you +2 daily comms, but only the first (next time, there is not bonus mission).