The answers are -
Yes, and Yes, and depends 
The subject of material placement, cost vs. performance vs. aesthetics and function is indeed a complication one. Too difficult I would say to generalize a one-size-fits-all formula for application and use.
Overall, the first things to determine that affects material selection I would say is the price point, category and market focus for the shoe. A top performance athletic (say basketball or running) shoe would be spec’d with different things in mind than a value/entry priced lifestyle shoe. Different brands also likely have different standards of quality, price, performance etc and may weight factors differently.
Ultimately in any application, there are trade-offs and compromises. Even in top performance footwear, there is an element of cost targeting that must be followed, and perhaps higher performance standards that affect aesthetic considerations. In lower priced footwear, performance may not be as much of an issue, but cost and aesthetics may be driving factors.
In general, the best way I could suggest to get a handle on all these things is to look at footwear on the market and look for the commonalities across brands, categories, designs, etc. If you look specific to one category (ie. BBall) you will likely find that certain materials are commonly used for certain parts (ie. mesh types for lining, abrasion resistant PUs for toecaps), and get some understanding on the factors involved.
The costing aspect of material application however is quite a bit more complicated (with microfibre vs. non-woven backing PUs, PVCS, a wide variety of suppliers, effect of volumes, etc.) and without in-industry experience is pretty much impossible to get much of a handle on. Basics of course you should again be able to pick up by seeing whats out there. You wont find too many 100% Aligator leather shoes at Walmart for 19.99… 
best advice of all…keep asking questions like these!
R