As others have suggested, use the shields to produce aerodynamic lift. Now you’ve got the best of both worlds. The issues at that point are:
Balancing the gameplay.
Making it look good.
As I see it, the gameplay balance should originate in the idea that shields in atmosphere draw a lot of extra power. This requires pilots to reduce power to other systems. But if high power on shields happens to also provide the ability to shape them essentially for free (on small ships) then pilots would tend to compromise thrusters because they can get better energy management from an aerodynamic shield shape. The larger the ship, the more prohibitive the power requirements become to shaping shields. Capitals just don’t ever do it.
Other things are possible such as eroding thruster performance in atmospheres. Like shields, they could work best in a hard vacuum. By reducing thruster performance on a 10g interceptor, you might reduce it to a 2g interceptor in a sea level atmosphere. Give it those shaped shields and you’ve got an explanation as to why it just became the equivalent of an F-22 in performance.
In terms of artwork, the shields would be translucent models of aerodynamic shapes. In theory, you could morph between a standard oblong shield and a shaped sharp-edged aerodynamic shield depending on the energy that you’re willing to put into the shield shape. Lift and drag changes would also interpolate.
Continuing with artwork, have the forward facets of the shield go more and more opaque according to the atmospheric pressure on them. So imagine that I’m trying to make a very high speed run through atmosphere in my interceptor without regard to weapons or thrusters. I’ve balanced energy such that I’ve got a highly-aerodynamic shape on my ship and a ton of thrust. I’m going so fast that my F-22 aerodynamic shape is glowing brightly, but only on the front. The rest of the shape fades out towards the back.
Note that when I say F-22, I just mean sharp leading edges and a cool overall shape. There would be no control surfaces, bubble canopies, air intakes, etc. Perhaps a B-2 would be a better shape to reference.
There are many things that don’t make any sense in the Battlescape universe. It’s a question of whether the chosen fiction is appealing to the customer base.