I think that mod-specific graphics belong in the mods... just have the LNP fish out the appropriate graphics from the mods/raw/graphics folder during the merge process.
Now, that opinion is based on a couple assumptions that I want to verify with the experts in the room:
1. There are more LNP players who use multiple graphics packs and zero/one mods than there are LNP players who use multiple mods and zero/one graphics packs.
2. Mods will be a separate download from the LNP.
Though not essential, the case is stronger if the major graphics packs are going to remain bundled with the LNP.
While it's better to have a simple solution than a complex one, the complexity largely falls on the mod authors, graphic artists and pack maintainers (rather than players), so as far as I'm concerned technical complexity is not a major concern.
So, the reasoning for keeping graphics-pack-specific files in a mod rather than mod-specific files in a graphics-pack is to minimize the amount of content that gets downloaded and never used.
The Earth Strikes Back! contains about 7 KB of images for creature graphics (out of 312KB). Even if I went overboard and made twenty different versions and they were different enough to get no gains from ZIP compression, that's still adds less than 50% to the size of the pack. This is about the same amount of space as if each graphics pack included its own graphics for
The Earth Strikes Back!, but with the crucial difference that the content is only downloaded by people who choose to sample/play the mod.
For reasons that elude me, somewhat less than 100% of LNP players use my mod
Therefore, it makes sense to package extended graphics content with the mod than with the graphics pack. As the amount of graphic content goes up in a mod, the potential impact on non-users increases.
Even if the LNP were split up so that graphics packs are downloaded separately (perhaps upon first selection in the GUI), the same reasoning holds. In fact I would suggest the LNP go to a fetch-on-first-use model for both graphics packs and mods, with some option to pre-fetch for those who don't play connected to the Internet (How do you survive without the wiki?!).