To me (unless I'm practicing scales) 3nps and Box form (3nps on most string 2nps on others) are completely interchangeable. There are times when I want a more fluid sound I might use 3nps but I could most likely get the same effect with box form most of the time. There was a time when I was all about the box form (15 years ago) however as my understanding of the fretboard grew I tried to get rid of that bias.
The point I'm trying to make is that its not that one or the other that is better or worse they are just different techniques that need to be learned and applied. Also if you are going through the trouble of learning 3nps patterns you might also want to try some less used, but sometimes useful, fingerings such as: 2nps, 4nps, and single string scale techniques. You can get an idea of how these techniques work in this
Guitar Scale Lesson.
BTW if any of you are wondering how to play these 3nps scale patterns or the box patterns for any Major, Natural Minor, or Harmonic Minor key check out my
Scales in Tab application it should be helpful.