Is the third nacelle just for look or is there a practical purpose?
It's based on the original Franz Joseph design from the 70's, the
Federation-Class Dreadnaught, which had a third engine. IIRC, the idea was that adding additional engines to the system would increase the ability for the ship to warp space around it, making it "move faster" than double-engine ships. Roddenberry decanonized it when he put out his "laws of starship design", one of which mentioned that starships may only have engines "in pairs", and in full view of each other, unobstructed by other hull structures. I'm paraphrasing, but that's the general gist. FJ's
Saladin-Class Destroyer and
Hermes-Class Scout suffered a similar apocryphal fate at the hands of Roddenberry's infamous memo typewriter.
As for later TNG-based designs that seem to violate the "in pairs" rule, like the "All Good Things" Enterprise-D and the "Best of Both Worlds"
Niagara and
Freedom, it has been postulated that all Galaxy-style "star drive" engines have twin warp coils in them. This is evidenced by two distinct red lights in the Bussard collector in the front of each nacelle. So, ships like the regular TNG Enterprise-D actually have the equivalent of 4 TOS-era nacelles and the "All Good Things" version technically had 6, not 3.
The
Hutzel kitbash from DS9 has Excelsior-style engines and could be argued that it has upgraded nacelles with twin coils as well in the post-transwarp era.
Explaining away the single- and three-engine ships in the new JJ Abrams movies are easier:
A) They are all likely operating under different technical and physical principals than their Prime-Universe counterparts as evidenced by their beer-brewery engine room and massive spherical warp reactor (and a larger amount of pulse-phaser vs. beam-phaser weapons),
B) They are considerably bigger than their Prime-Universe counterparts and have plenty of room for twin coils, and most importantly...
C) They don't give 2 rat-turds in a rain barrel about Roddenberry's bullshit laws of starship design.