Well, I've been thinking about starting a whole separate thread about this, but it's one of the many things that doesn't make much sense in the treknological continuity. I've always figured that the warp core should be either in the nacelles (where the fuel is delivered to them from the pylons and the engineering section) or in the engineering hull so it can be close to the fuel supply.
Having them in the nacelles would make alot more sense in light of the fact that exploding warp cores is the number one killer of starships (behind that pesky Starboard Power Coupling, of course). But if you only have the one engine that requires a whole lot of babysitting, then the nacelles are really just the impellers where the warp core is the actual power plant.
To be perfectly honest, I wouldn't be surprised if both configurations exist in various ships/races/designs. Some of the smaller shuttlecraft probably have warp cores built into the nacelle cones, and actually I'd be shocked if the Romulan Warbird didn't have that exact configuration.