I want to know which are the best missions to farm materials both for ghoul and quinque ones. 
I'm still a few levels away(3) to unlocking hard mode, but does it affect drops? Or what does it change exactly?

Thanks in advance to everyone who helps

This is very simple.
Just buy speed boost item on shop and attach it to your jet. With little effort, you can easily get SSS on every missions.
And try to raise your jet to move faster whenever possible, and try avoiding hitting any walls that will decrease your speed shortly.