Will charging up Destruction Master spell break Invisibility?

No i don't think it will..i would have to test it but i think you have to release the fireball to break Invisibility.

No, and you can draw a weapon but not attack as well. It's loosing the spell or striking that ends the effect.
Also remember, the light from having spells prepared in your hands does not figure into sneak chances.

Yep.

This is especially fun when you have a "stealth mage" type character. Muffle + Invisibility to sneak into an encampment, then fire off a Blizzard or Firestorm

I'm glad for this thread as due to Dunmer now being top at destruction magic and also Dunmer have always been the main race associated with assassins (Morag Tong which spawned Dark Brotherhood. Many Dunmer worship Daedric god associated with assassins etc), I now want to make a Dunmer mage assassin

And if you don't do illusion or alchemy, Become Ethereal is a good way to let enemies gather around you for Firestorm

With the muffle perk, you can sneak attack your foes. Unfortunately, you don't deal bonus damage. Why not? There should be a perk that gives you a bonus. Perhaps one that branches directly above said perk?

or even a new form of destruction (as in fire, ice & shock) designed just for stealth players. Rubbish when in open combat but deadly when hidden (much like a dagger in 1-2-1 melee combat).

That could be the return of "touch" spells. That's not a bad idea.