Quote: "You shouldn't use n-gons in your models. This isn't something that you can argue either way for, you SHOULDN'T."
Sure you should, especially in technical models such as this weapon.
Quote: "There are a bunch of reasons, including animation and meshsmooth results, workflow in your chosen 3d program, and higher poly > lower poly normal mapping"
None of these are negative points and some aren't even points. I don't know what type of animation you're using but last I checked both the Skin and Physique modifiers worked only on the vertices of the model, as such, how the underlying geometry is constructed doesn't matter at all. Yes meshsmooth results do change based on how your polygons are constructed, after all, this does work on edges(of polygons). However, if you were to make a model intended to be meshsmoothed you would know this and you wouldn't deliberately make your extruded/cut edges(to be meshsmoothed) into giant polygons.
For example:
These meshes are the same when triangulated, but the left one has polygons which use far more verts.
When meshsmoothed:
As you can see, the one using quads has the desired result, but this is because meshsmooth works on edges, if I were to make such a mesh I would never use polygons with more than 4 verts in such a place, but this doesn't mean such polygons can't be used when meshsmoothing. Thus this point is moot.
Also the workflow is faster with polygons with more than 4 verts anyway(most of the time), you have to do less selection to do certain things. Besides quads ARE polygons so what are you even complaining about? The only difference between a quad and a cylinder cap(with more than 4 sides) is the amount of vertices it has.
And what of the polygon mapping to a lower detail mesh? Usually you only use polygons with many verts on flat, or flat-ish surfaces, thus such mapping wouldn't have any bearing on this.
Quote: "but the main point is that you have no idea how the model is actually layed out with an n-gon, and you lose that control."
Of course you do, you do realise these 3D applications draw traingles in your viewport, thus they have to be constructed of triangles somehow. If you've ever gone beyond the basics of max you'd know that you have the ability to view the triangulation of a polygon without actually triangulating it. If you go to your lovely Editable Poly modifier, go to edge mode and Turn or Edit Tri you can see the triangulation. If the triangle order is causing you issues during animation then you could just turn the edge, like you would if your model was fully triangulated. You still get this issue with quads you know.
Quote: "If you look at any model made for industry work there are no n-gons, and they are modeled with quads, and triangles where appropriate."
A quad is a polygon so yes they are. Here's one example(
http://features.cgsociety.org/story_custom.php?story_id=4762&page=2) of industry work that uses polygons, it wasn't that easy finding a wireframe render though. If you scroll down to the video the right of the 'Priorities' heading and scroll the video to about 3/4, until it says Wireframe Singstar(NOT the gun), you can clearly see several polygons beyond quads used in the upper armour.
So to conclude: Polygons are very useful, they are only bad if you don't know how to model and mess something up, they can speed up workflow and really aid in selections of meshes, UV mapping, visualizing the mesh etc etc.
And remember that I'm not saying you should make as many large polygons as possible, but that having them isn't necessarily a bad thing, and doing things like tracking them down and removing them when they aren't a decrement to the mesh is stupid.