Well with the Motion Picture they did to an extent. They added in details that were missing, and even CGIed V'ger so that the viewer could see the entire vessel. Not to mention the revamped Klingon battle sequence in the beginning. The rest only had minion changes mostly adding in the deleted scenes which does make me somewhat sad but it's something.
I'll buy the torpedo rooms being heavily armored to guard aginst such things, but I figure the explosion would completely wreck the torpedo room proper, with a very small chance of the blast getting into the magazine. (I figure the refit Constitution-class had to have magazines somewhere based on that scene in STVI where Bones and Spock perform 'surgery' on a torpedo.)
The only issue I had with the Reliant blasting the torpedo room in 'round 2' of the battle, was that we saw some poor crewman going up in flames and the whole compartment being filled with fire.
...And then when the ship's company comes together to launch Spock's coffin, there's no sign of damage. Not even a soot mark to be seen. Take a look at the phaser hitting the Enterprise's hull: it 'walked' along to the airlock hatch that Kirk's party used to board the ship. Even if that hatch had two sets of doors to form a viable EVA point, you're talking about serious structural damage.
I suppose that 'dramatic licence' takes precedence, though.
Unless they had very good DC Teams, and I doubt it, with a crew of cadets, or, the explosions were localized to the torpedo room that was knocked out of action... take your pick, because the external shot of the launch of Spock's coffin clearly indicates that the starboard tube (facing forward) was operational following the battle.
Torpedoes are stored on racks in a magazine however they are completely harmless. There payloads are put in from the warp core as soon as they are about to be launched. However if a torpedo was to explode in one the compartments then I don't think it would still wreck both of them. Hence the separation, keep at least one going until that too gets hit.