The question regarding windows (to make them transparent or not transparent - that is the question) is an interesting one that, I think, deserves some thought. My own opinion is that, as in so many other cases, words like "always" and "never" are inappropriate, and that the "best" solution varies case by case.
I tend to come at such things from the perspective of a sailing ship model enthusiast. People like me tend to work in considerably larger scales than 1/350, but some, at least, of the principles we think about are just as applicable to smaller scales.
Sailing ship modelers have been taking it pretty much for granted for at least a couple of centuries that a good model has glass (or clear plastic) in its windows. Nothing else looks as good. Once in a while somebody uses a cystoscope or x-ray machine to examine the interior of an old "Admiralty model" and finds some fascinating stuff inside it - stuff that, in many cases, doesn't show through the windows.
I recall a restoration job on a model at the maritime museum where I used to work. The model was of the late-nineteenth-century passenger liner Britannic; it was on 1/48 scale, and measured about fifteen feet long. I happened to catch sight of something in one of the portholes, which were made of glass. I started polishing them, and shined a flashlight through them. I discovered that the entire first-class dining room was fitted out - complete with tables, a piano, and a set of wineglasses stowed upside down on the overhead. In all honesty, though, I think the other staff members and I were the first people in at least fifty years to see all that detail - and, though I wrote something in the label urging the public to look through the portholes, with the model sitting in its big glass case it's almost impossible to see it all now.
I certainly agree that, if the layout of the windows is such that they let light come through the model in a way that's noticeably unrealistic (i.e., like seeing through a house), something ought to be done about that. I'm inclined to think, though, that putting some sort of partition in the interior to interrupt the light is generally preferable to making the windows themselves opaque.
Here's a picture of my model of the Continental frigate Hancock (which regular Forum participants, I'm sure, are sick of looking at by now): http://www.hmsvictoryscalemodels.be/JohnTilleyHancock/photos/photo9.html .
The scale is 3/32"=1'; the transom is about 3" wide. The windows are made of clear plastic, and I contend that the model would look hoaky if they weren't. In this particular case, though, after taking a careful look at the layout of the windows and the rest of the hull, I concluded that putting any detail inside the windows would be a waste of time. Anybody who takes the model out of its case (bad idea) and shines a flashlight through the transom windows may, barely, be able to make out a small sign on a post in the middle of the captain's cabin that reads "Sorry, no interior detail." So far as I know, though, nobody but me has seen it yet.
I also remember looking admiringly at a superb, 1/48-scale destroyer that got brought to one of our club meetings years ago. It was one of the most meticulously detailed models I've ever seen - down to and including the corrugations on the trash cans in the racks on the fantail. But to my eye the illusion was spoiled, to some (not very big) extent, by the fact that the portholes in the pilothouse were represented by circles of gloss black paint. To me, that approach looked jarringly inconsistent. Suppose, though, that the builder of that model had made the windows out of clear plastic, and had included all the bridge equipment inside - the wheel, engine room telegraph, compass, etc. If I'd craned my neck around to just the right angle, and the light had been shining just right, would I have been able to see them? Maybe, but I doubt it. If the destroyer, rather than a round-bridge Fletcher-class ship, had been a Mahan-class one with larger, rectangular windows, would I have been able to see the equipment inside? Probably so.
In 1/700 scale those black bridge windows probably wouldn't have bothered me in the least. In 1/350 - I don't know. Reviews of aircraft kits often comment that the manufacturers have wasted effort on interior details that are, to all intents and purposes, invisible through the canopies and windows - especially in small scales. Some companies make the windows of 1/144-scale airliners out of clear plastic, and others represent them with black decals. But scarcely any such kits have seats, overhead bins, movie screens, etc. The windows, even if they're transparent, simply are too small to justify such treatment.
Someday in the fairly near future I hope to tackle the beautiful new Dragon Gleaves-class destroyer in 1/350. It has small, round pilothouse ports, which are represented by countersunk circles less than 1/32" in diameter. I haven't made up my mind yet; my inclination is to drill them out and fill them with something like Micro Crystal-Clear, but I reserve the right to change my mind and paint them gloss black. (I certainly think making windows shiny is generally a good idea.) I can say with certainty, however, that I am not going to put the bridge equipment inside.
At least one of the manufacturers, Aoshima, has started advertising that some of its 1/700 and 1/350 kits have "clear bridges." I haven't bought any of those particular kits, so I can't comment from first-hand experience, but I'm inclined to think the idea is sound. It certainly makes as much sense as the current trend of molding 1/700 aircraft and ships' boats in clear plastic, so they can have clear canopies when they're finished. How does one explain the fact that the windows in the island of a carrier are solid black, while the canopies of the Helldiver sitting on the flight deck half an inch away are transparent? (That's the sort of thing my wife would notice.)
I don't pretend to have a universal answer to this question; I don't think there is one. I do suggest that the question is worth serious, case-by-case consideration.