Just adding the individual mod tags and not giving them their own section I think would be enough. It would act as a far superior forum searching tool. I'm not going to reference a certain not-safe-for-work site that does tagging really well, but this is sort of on those lines, and it's already known to work well. You could also do some tag integration; like in the mod-list in-game, have each big mod's tag appear so people know what to search for. I don't know how you'd moderate that side of it but yeah.
I do have a question though.. will this game be released on steam at some point? The steam workshop is pretty good at making mod installation and maintenance easy. Do you plan on utilising it? There is a problem if that is the plan though; it'll create a divide in your community. Just thought I'd mention it.