Parts of mesh invisible when joined.

I had something similar happen with a mesh yesterday. Check the UV-map and see if the UVs for both parts of the table are there. In my mesh the UVs for the joined mesh snapped together into a tiny point in the left bottom corner when I joined the two parts, causing the joined part to become see-through (ended up fixing it another way, though). 

If both parts retain UVs in the proper place when joined, it's probably just the materials joining together and applying the main material for the main mesh (the last selected, I think?). If so, the texture you apply in S4S should still work fine, and so should the texture ingame. The textures/materials in Blender can be a bit moody, and frequently do weird things, but if the UVmap is fine the texture should work. 

One trick you can do if Blender is being a problem with textures is simply to finalize the mesh in Blender, export to S4S, finalize the item in S4S and apply a texture there, then export the item as a Blender file and reopen it. Then it should have a working texture and proper names and all.