Would it be possible to have a run category/subcategory using nitrox and multiplayer. i.e. running duo's all egg%.

The speedrunning leaderboards are for the game as distributed by the developers. Nitrox fundamentally modifies the game in ways not officially supported, is not guaranteed to be stable for all users (to an even lesser extent than the base game), and is not available on all platforms. It would not be appropriate to add a category for multiplayer unless officially supported.