Lightmaps are the colored images generated by RAD that get put over the maps faces to simulate lighting. Obviously, blending two textures for every face that's being rendered takes some more time than just covering them with one texture (ak. fullbright).
Yes, maps will run differently on different machines. Poly counts are a usefull guide to make predicting the fps on other machines easier. They're no strict guidelines that every mapper should abide, though.
For Source, many more factors impact fps. The budget panel shows you where the engine spends it's time which makes it easier to pinpoint problems (like cutting down on dynamic lighting, or ragdolls/physics objects, or indeed cutting down on sheer polycount).
As for epoly's, these are easier to handle (exactly because they don't have an additional texture (lightmap)).
The average ratio between epoly and wpoly seems to be 10:1 or 12:1 or so.
If you set yourself a polybudget of 1200, you could put in 1000 wpoly and 2000 epoly.