"Or vice versa, as we only ever see the domes blowing, in two TNG episodes, before the nacelle style changes to domes-only and we see them suck in ST:INS"
IMHO, you are applying way too much retroactive continuity to identify the function of the component of a ship that's 100 years older.
Just today there was a suggestion at Trek BBS to visit this link: http://www.slightlywarped.com/crapfa...rek_photos.htm
Unfortunately you have to scroll down a bit, but there's a rare shot of what I believe to be the "Phase II" Enterprise
prior to TMP and this is a shot I had not seen before, revealing a significant different warp nacelle design (prior to TMP).
No sinks at the front of the caps, just a large panel area left and right (which eventually became these plasma emergency flush vents on the support pylons).
At this design stage there are either reactors in front of the nacelles (to explain the odd placing of the emergency flush vents) or these panels are improved / enlarge space matter intakes.
A clear hint, IMHO, we are looking at a design evolution towards
the Bussard ramscoops of the TNG era...