[Suicide Junkie]

1) Only Armor can protect you against unexpected and/or natural phenomena. Shields are only raised during battle. Just layer on the armor, and build a repair base on the other side.

2) Unless you control >10% of the galaxy or are partners with everybody, destroying black holes is probably too expensive ($$$, research points & time) for you. Better to just go for a low tech solution (armored repair ship + armored ships) If you are really serious about "fixing" your system, and have 5 years to spare, research Stellar Manip (under astrophysics) way up. IMO, a quick armor & repair then shields & weapons would be better research.

3) Somewhat. Once you know how to solve your BH problem, theres nothing to worry about. If you don't know, you better ask, or spend some time to figure it out.
I like BHs, since they provide a great buffer against powerful enemies, while you're fighting for your life on the other side of your empire.
- Low Tech soln: Armor + repairship
- High Tech soln: Quantum InVersion beam + wormhole creaters.

4) The storms you can create only hide your ships. Natural storms can have many special abilities. With a storm, you can hide planets/ships/bases/stars. Maybe not stars, but maybe.