The only drawback is when you destroy an engine subsystem, the glowpoint doesn't vanish. It requires the SEXP to disable it once it is destroyed. Area lighting could solve this (since it saves FREDders and modders a lot of time), but for the moment, the engine doesn't have support for this.
I can think of several ways to make this easier(LUA scripting, perhaps a flag for submodels with glowpoints that have overrides), area lights would have to be handled the same way glowpoint overrides would be, they just wouldn't have a visual object in game like glowpoints. The engine doesn't need to support area lights when it has a similar feature that is just as functional.
I know lens flares only apply to the stars (at the moment), and this is a issue. We'd would like to expand it to include glows from ships, but care must be taken to reduce over-use of lens flare effects as seen in the 2012 Total Recall remake, whose movie universe being reused as a setting in my Shattered Stars campaign.
Applying lens flares to glow maps would be next to impossible without generating and rendering the lens flares based on the space taken up by the glow maps in the view port (something UE4 is capable of), and this would be fairly destructive to performance in FreeSpace, so I don't think it's going to happen any time soon, especially since there's not even support for the OpenGL Core Profile.
Edit: This is also the wrong thread to discuss rendering features that aren't currently present in FSO. This thread is purely for modeled thruster updates and I would like to keep it as such.