You use q3bsp by using a tool called q3map2 to compile your map.
In short, Quake 1 maps use .wad files for textures, a Quake 1 map compiler, and Radiant set to "Quake" with the Quake gamepack. Very logical
Quake 3 maps use "shaders" (aka materials) for textures, a Quake 3 map compiler, and Radiant set to something other than "Quake" with something other than the Quake gamepack (probably "Darkplaces"). The gamepack includes an entity def file which gives you the selection of map entities for that game, as well as some format definitions etc.
I don't use q3bsp + DP for mapping, so others might give you better advice.
I have yet to hear a good description of what clipnodes are, except that they're obviously used for clipping and your map is filled with them. From a mapper perspective, your clipnodes count rises sky-high when you include an unusual amount of brush-based detail and wide open spaces combined (e.g. e1m2rq). The vertex limit, on the other hand, is usually broken by having a physically humungous map (e.g. e2m1rq) - lots of triangle terrain helps you break it quicker.
I don't think mapmodels count towards the BSP format limits since they're not physically part of the BSP. They will only add to the vertex count if you somehow convert them to .map format and physically paste them into the map (as opposed to loading them at runtime via misc_model or the like).
I don't know how well DP handles version 2 IQMs, Lord Havoc is the person to ask there.