With a typical soft bag, it's a pretty minute difference unless you're getting a severe headwind or hefty crosswind. Typically they tuck in well enough behind your legs to keep notable effects down.
I never had the hard cases on the TW but I'd imagine it might be a bit more noticeable there, and while I originally liked the idea of those, I don't think the risk of breaking an ankle on the trails with them would be worth that plus the high cost.
I guess I should add that the weight is going to do more than the aerodynamics, I'd imagine. And even so, it would probably just take you longer to reach top speed. A big top bag with a lot of weight could also get a wobble going, but maybe not at TW speeds.