thank you for testing the exporter! That's great job! Any bug reports let me to concentrate on improving script functionality. IMHO it's normal work process

1) Concerning your first problem I designed exporter to look for texture file in ".../nexuiz/data/textures" subfolder. It is because it is the same in "pk3" package format. Actually you lead me to an idea to take texture name and it's folder as a material description if it isn't on a normal path (e.i. in subfolder of ".../nexuiz/data/textures")
2) As for your second post these values meaning is the following. Because of floating point number format limited precission sometimes when I calculate if mesh is convex or not for faces lying in one and the same plane it might show anything (convex, concave or planar). Due to this problem I do the following. I scale all dimensions on scale supplied and round them to integers. Also it's good for me because I like meters but not units. I've decided that 32 is good approach, e.i. if edge size in Blender is 1 it would be 32 units in NetRadiant after export.
Concerning extrude height it is a height of a prism when concave mesh is splitted into individual prisms. Look (5) for details.
3) Yap, it's a bug! I'll fix it and submit with a fixed version as soon as I can!
4) No hierarchy wouldn't help. The problem is in text terminal output. It's my drawback! I'll make text echo output optional. I expect it to work much faster after disabling it. I've already met such a problem in my previous works. I believe it's the same. I don't think that OctTree subdivisioning is the case.
5) It might be because one or several meshes are not convex. It informs you about that, makes these meshes "ignored" (look at game logic section there would be such a property after export try) and creates as many prisms as faces number in each mesh.
In other words exporter substitute convex meshes with their individual faces extruded on a "extrude height" distance.
Thank you again for exporter testing. It's very useful! Please inform me about any bugs/ wishes/suggestions!!!