Auto Combat : Strong vs Weak Selection

Generally yes; the sole exception is that the fighter will often target flak frigates for some reason.  Generally the most important management is to keep fighters, bombers, and light frigates clear of danger.  These units are somewhat fragile so you need to maneuver them around dangers to keep them alive.

Yeah the unit AI tends to do a good job of that (much better than any other game I've played), though there are certain situations where you'll want to focus fire instead. That said, fleets always perform better if you can micromanage them, so if its an important battle you should probably micro it anyways.

1) Is it possible to attack target by type? Eg. I want my fighter squadron to attack 3 bomber squadrons. How do I select the targets so that the figher squadron will attack all the bomber squadrons without Shift-Right-Clicking all the different bombers squadrons?

2) When the units are displayed in stacks of 20 on the left panel, and I do a right click on it, does my unit attack all the 20 units in the stack or just one unit?

Thanks!

Bombers are the preferred targets for fighters.  You don't need to worry if this is your preferred target.  Otherwise, shift-click is your only solution.

I believe they will focus on one unit in the target stack.

Yes this is one of the to do list for next patches i believe. 

Your units most of the time focus fire on one ship but not 100% of the time. And when that ship is killed they go back to the script (read prefer and attack ship set up by devs) and you need to set command again.

You can queue focus fire by shift-right clicking on the targets you want dead. I just figured that out yesterday.

Yes you can but if you have them stacked by 10 they will attack only 1 st ship and then move on. They won't go throught all 10 ships and then attack what you selected next....

If the Devs indeed alter the stack attack protocol in a future patch it would be a welcome relief when trying to micro a large battle ball.