I suggest redoing item categories "Surface-only items", "Dual-use items" and "Underwater-only items". When equipping the craft, these categories are not useful. When going on a mission, if you use the item filter you need to check both dual-use and the environment-specific item list to figure out what you want to bring along.
At least from the point of view of equipping the craft, it would be far more useful to have categories "underwater items" and "surface items" (i.e. items that work on the surface, and items that work underwater). Dual items would belong to both categories. This way you would only need to browse list once. This is how it has been done in X-Com Files, for example (items may have even half a dozen categories for different mission types).
If there is some specific use for current division of items, the existing categories could be kept and "Both surface and dual-use items" and "Both underwater and dual-use items" categories added instead. But I suppose this would just cause more confusion.