Damn that Warp field geometry.
Ok, that's the reason for nacelles "now".
Back in the 60s when the "Starship class" design was made (later known as "Constitution class", noone knew of anything like a Warp field / bubble.
So that never was the reason for making nacelles.
In fact, the idea of protecting the ship from hazardous "effects" was rather the reason as those theories were around at that time.
That "radiation" (as you said, gamma radiation or electromagnetic waves don't get weaker in vacuum) may consist in particels that loose there effect very fast or it could be that it was not about radiation, but about EM
fields. Such a field would have certain dimensions. Building the nacelles far enough away from the crew compartments would protect it from that field.
Remember, Klingon and Romulan starships in TOS had Nacelles as well.
So it might be that originally it was thought, if a ship uses the same propulsion as the USS Enterprise, it would need nacelles.
At last it is again about inconsistencies beetween TNG+ and TOS.
So when talking about Fleet Operations era, the need for nacelles would be due to Warp field geometry problems.
