Cotton thread is generally weaker than synthetic and often used in things like repro denim (just for the sake of being authentic) or with very delicate fabrics. A fair amount of stuff, high or low end, is made with synthetic thread. The shrinking issue isn't a huge deal, since cotton thread/fabric would probably shrink at different rates due to different constructions. Higher end stuff should have preshrunk fabric before cutting anyway, ensuring that's not a huge issue. I've really never seen that be too much of a problem at any price point, actually.
Also, designers often spend a fair amount of time considering what color/material/pricepoint of thread to use.