I can't argue about the problems with TNG but I did voice my concerns at the time, trust me!
This model was used, reused, and used again. It was originally prepped for STIII, as a mercenary vessel, taking a spy back to the Klingons with the Genesis data (don't get me started on the protomatter MacGuffin!) used in several Nxt Gen episodes, including the one of which you spoke. If I recall, that model from the same season was re-lit to suggest a different ship.
The Merchant ship was hoisted a couple of engines from a Federation ship, glued on backwards, and relit for a Sheliak vessel in another episode, and then used again in Voyager as a Vidian ship. Neither of these uses fooled anyone, nor made much logical sense. It was recolored tan and used in DS9 quite a bit as a transport, which did make more sense.
The original coloring, a purplish-pink, was grafted from a theme developed by one of the art people from STTMP, in which he suggested that inferior ores were used in civilian vessels, and this coloration would communicate that (hence the civilian Vulcan shuttle). The reasoning for the exposed areas was two-fold; hull plating is expensive and difficult to maintain for reasons more than its initial cost; ships release radiation regularly and only expensive, sophisticated hull material allows a controlled bleed of it (materials that poorer vessel owners cannot secure) and the removal of the plating and hull to repair in frequent dock maintenance added to expense and time in dock. A quicker turnaround was possible when the exposed areas were accessible to repair and replacement.
Federation ships were supposed to reflect the pinnacle of technology; hence enclosed. This was a hold-over from Jefferies, who felt that more advanced ships would be smoother and contained. They were somewhat more repairable from inside, but the real difference was that the covering of components reflected sophisticated design and material use. Audiences, use to Star Wars, often prefer exposed, greebe-ridden designs but this conflicted with the logic of the Trek design. The TOS hull, appearing streamlined and clean, was the original designer's vision ( a man with some aeronautical engineering background); it reflected advanced ceramics covering energy-charged machinery.
Interesting, the need for protecting radiation bleeding tech would be minimized in space by cost conscious-owners, due to how little any debris particles or radiation-threat typically would exist outside of an atmosphere, for a ship protected by shields and navigational deflectors. Energy fields that have to be there, to permit warp travel and atmospheric skimming, are cheaper than hull plating! Though physical barriers would benefit military ships engaging in conflict, which use travel pods and work bees for the external repair of damaged systems or for maintenance, that are too large or complex for internal access (or which were so energy intensive as too require heavy internal physical shield barriers), civilian ships typically wouldn't require such extravagance. Today we see cost-cutting efforts as typical. A Trek ship is a very large expense i the storyline, similar to the vessels of the period of the Age of Sail, for an owner or firm.
The less invest the owner, or the more on its last legs was the ship, the more exposed ( the logic went) would be the vessel's interior, ergo the more greebes!
Nxt Gen & DS9 followed this logic through their runs, more or less.
One thing to remember is that the tech of vessels on Trek was very different than found on most sci-fy. Vessels were devices built around energy plants. Most fiction approaches vessels as modular components strung together, like the way engineering of modern tech combines power-plants, functional devices, etc. Trek design was supposed to reflect unified energy systems that components and habitation areas were added to, within the limits of what a warp field would permit; which it why power could be diverted from impulse to---, or from warp to---. The idea was that the ship was a series of cooperating power plants that bled off energy to systems, using all energy as possible with as little waste as possible. Even then, hazardous radiation was always a factor in the background, even in TOS, and life sustaining compartments had to be very carefully segregated. During the original series, the logic was that no habitable area could exist between the powerful warp nacelles of a ship as capable as a Constitution class vessel.
Nonmilitary vessels bled radiation off without barrier, both to save money and because being stealthy wasn't as much as an issue as a military vessel might warrant. The exposed areas of the merchantman vessel probably contributed to a more visible sensor signature than a Constitution-class vessel, despite the latter ship's superior size and power output!
Space also serves well as a natural coolant.
There were a lot of discussions with NASA techs during the original run, with less technobabble rationalization...