1) On larger maps, the Sova probably isn't your best selection.  Use the Akkan instead to give you a stronger economic advantage, and bring out the Sova later.  The Sova is very much a rush and counter-rush type of capital ship, and the skills you select are based on how you intend to use it.  You usually do not want to balance all three skills, and want to focus on any two.  Generally speaking your first skill should be either Embargo or Missile Batteries; the only advantage of heavy strike craft is that it costs no antimatter, so it should never be your top priority ability.

Focusing on missile batteries and heavy strike craft is what I call the "brawler" build.  It's an ideal capital ship for defending against early enemy incursion and it's great for leading direct assaults.  Needless to say, it's about pure brute force and maximizing your abillity to pummel the enemy. 

Alternately, you have Embargo and Missile Batteries as a very aggressive offensive built.  The approach here is to directly assault key worlds and suppress the enemy's response with embargo while using missile platforms to give you the military edge.  The trouble with this approach is that you often will run dry of antimatter and be unable to balance both abilities.  For more flighty Sovas, a combination of embargo and heavy strike craft can be useful; this gives you added combat value without the extra antimatter cost.  Unfortunately, the loss of missile platforms will greatly decrease the combat value of your Sova, so this convenience comes at a price.

2) No; they only attack frigates.  The Sova has some of the weakest bombard capabilities of any capital ship in the game, which is one of its primary weaknesses.

The Vulkoras has an ability that deploys siege platforms, however.  It's actually a very dangerous ability, and a properly specced Vulkoras is the best siege weapon in the game, vastly eclipsing what siege frigates can achieve.

3) Only for the Sova itself; other friendlies in the gravity well do not gain this benefit.

YMMV

Those are both great abilities, and frankly I think there's a lot of personal preference in Sova builds.  I've run every 2-selection combination of abilities as Sovas and been quite satisfied.

On bigger maps, I'd be more inclined to go with Akkan or Marza.  Marza can clear militia faster and maxed out raze planet and (even better) missile barrage can be invaluable assets for the first battle.  Sova is great for clearing militia, but you don't exactly get a massive boon for raising one to high levels, which is what makes it a very dedicated rushing capital ship ship.