#1
Do these musicians study all these different tunings like Drop C and D sus9 Tunings etc before writing complicated pieces? or they randomly playing these new tunings until they stumble across something that sounds good?
#2
Combination of noodling and composition, bit like everyone else in every other tuning, really.

There is no simple answer, it depends on the artist. This probably doesn't belong here by the way.
#3
Well if you know the certain sound you're going for (which you should do really if you're a pro composer) like a dark gloomy sound, or a happy cheerful one, you should know which scales/modes to go for, and which notes are in those scales. Then just work out a tuning based on those notes.