Not a trekkie, do they ever land in atmosphere on these ships? You would want aerodynamics for that to reduce drag and thus heat, but I’m not familiar enough to know.
I guess they probably have good thermal protections with their future tech, though.
I was thinking more about atmospheric entry and exit than flying around in the atmosphere itself… but a bubble would be weird because fast-moving spheres would create pretty unstable drag and induce spin, iirc.