I have done that on occasion when I have screwed something up beyond being able to fix it, or if something is broken/missing from a kit made by a manufacturer that is either out of business or just difficult to get support from. Sure somebody can jump through all of the hoops to figure out how to get a replacement part, but like you said, sometimes its almost as costly as just getting another kit...not to mention that time is extremely valuable too. Buying 2 is something I actually do pretty regularly with aftermarket decals and some aftermarket items like Quinta cockpit sets...sometimes it takes a really long time to get replacements, and sometimes things like decals go out of print really quickly. I guess it depends on the circumstances, but I have definitely done this.
As for imperfections, I tend to feel the same way you do...something may not even be visible to other people, but I'll always know its there and it bugs me. Whether I fix it or not depends on the amount of effort its going to take. I have gotten pretty good at fixing paint damage lately. Also, there's always a bath in isopropyl alcohol and a scrub with a cheap electric toothbrush in those frequent (for me anyway) cases where you try a masking/painting technique that doesn't work the way you thought it would...done that one a lot.