There are the considerations with exterior aesthetics, but it's also about being able to maximize interior space and meet design criteria. A change in doctrine after Wolf 359 was to leave as small of a target profile/silhouette as possible, so ships started becoming more streamlined. This also lead to ships being able to travel faster because that lead to creating a more efficient warp bubble around the ships.

Out of universe, Roddenberry said the nacelles need to see each other, operated in pairs, and the bussard collectors (glowy red parts in front) need to have unobstructed view so they could collect materials from space.

A sphere is the ideal shape to distribute the force of the atmosphere inside the ship on the hull. A cube would not distribute the forces evenly and would need to be re-enforced in places.

According to the technical manual, the Enterprise-D looked aerodynamic because it made the warp field more efficient.

But yeah, as others have said, the rule of cool always applies.

The honest answer: Aerodynamic ships look cooler

I am not sure about how this phenomenon works in context of the warp drive where space-time itself is warped around the ship, but in universes with more conventional FTL mechanics where objects are contradictory to special relativity just accelerated to speeds beyond the speed of light, yes, aerodynamics do actually kinda come into play again.

Space isn't really a vacuum, it just is empty enough ao that we can mostly treat it like one. But space still contains a lot of particles, dust or debris for example, that with higher speeds, there is something very similar to an air reaistance, drag and all that.

However, there may be other factors that can be more important for a space craft design. If you are into absolutely overthinkinh such things, I can recommend Isaac Arthur on Youtube.

Not if it never encounters an atmosphere, but many sci-fi ships are supposedly capable of planetary landings.

If they ever need any sort of aerodynamics they could just shape the navigational shields.