"1. Can I give any ability to any object?"
Check SE4 Modding 101 Tutorial, chapter 16, linked in my sig.
"2. How many abilities can I give to ships/facilites/components?"
As many as you want to. There is probably a limit, but it is likely to be 255, so it won't ever be run into.
"3. Can I give the claok ability to a facility?How will it affect the planet or will it have no effect?"
It will not cloak the planet Last time I checked. You can use the Sector - Sight Obscuration ability on a facility, and that will cloak everything in the sector (planet, ships, bases, enemies, etc.).
EDIT:
Better turn my sig on when I make a reference to something in it...
[ June 30, 2003, 22:29: Message edited by: Imperator Fyron ]