Well, memory serves, that the nacelles generated radiation when being used that could be detrimental to crew, and so were located on pylons away from the main ship.

http://memory-alpha.org/en/wiki/Nacelle

This is common in Klingon Vessels, Romulan, and Vulcan ships. Ferengi vessels do not have the warp nacelles seperated, and possibly may use a slightly different type of war technology.