One kind of instrument where amplification always messes the sound up is flutes (transverse, endblown or fipple) - putting the mike inches from the sounding edge always picks up air noise that you'd never hear at normal listener distance. Most people who only know the Turkish ney from recordings or amplified performances will think its sound is mostly whoosh - in a real Sufi music performance, playing in a large room to an audience that knows how to shut up, you don't hear any air at all.

The folks who really understand that are the beatbox flute players. Using the mike as part of the instrument shows deeper understandng.