It basically boils down to how you view the role of the nacelles.
If you think they generate power, then the FJ dreadnought is the way to go, because with that third nacelle, you've got 33% more power right off the bat.
If you think the nacelles use power, a third nacelle is just one more exposed target and drain on the power systems, and you'd get more mileage out of just beefing up the standard two nacelles, reducing the ship's profile, and adding some more weapons. Plus, another warp nacelle would be something you'd want if you want more warp speed, or at least the ability to sustain high warp speeds for longer duration, and that's something you'd want more on a scout, destroyer, etc. (the Stargazer makes much more sense as a scout than the Hermes ever will), rather than a big battlewagon.
Yep, absolutely correct.
I see the roles of the nacelles as changing around the time of TMP. Prior to TMP, primary power generation was in the engines themselves. With TMP, primary power generation occurs in the hull (although there may be some additional power generation in the nacelles, we have no reason to believe this to be the case).
By the way, adding a third nacelle actually increases power generation by 50%... ie, with the added nacelle, instead of two, you get 150% of the total power generation (not counting auxiliary power - fusion reactors, in other words).
With the TMP-era model, the Federation (uprated) design actually had a second matter/antimatter reactor in the secondary hull, meaning that this ship had 200% of the power output of the Enterprise class. The additional nacelle would, at sublight at least, be nothing but a penalty, as you say, and would provide no additional power resources.
It's a major context shift between TOS and TMP. I, personally, think of this as the implementation of "First Federation" principles into Starfleet designs. Your mileage may vary...