I can answer 1 & 3

1) I think it's now at 20-22k cloak. However it still can be hacked from you if you're really unlucky.

3) Storage planets mostly and non-invincible planets that you are intent on keeping. Though it's only effective if no one else has it scanned.

http://galaxylegion.com/wiki/index.php/Scan_Blitz
consult this for the amounts of cloak you need on planets

Max the passive cloak on a planet.
25 interspacial fold generators and 4 Magnetosphere Charger
or
28 interspacial fold generators and 3 Magnetosphere Charger
Both give 3892 passive cloak before bonus.

Then you add those handful of artifacts that have a decent chunk of cloak with them
Gas vesicles, Dark anti-beacon, etc.

Then you add the % cloak modules like ergo sphere filters
Meta-Tuned Jammer Effect : Cloak +25% are also very nice but those are for the higher ranks.

Add researched cloak structures as needed

Basically cloak your best planets. How many planets you can afford to cloak is dependent upon how many dark badges you can get and how many fab plants you are hitting in your legion.