Yep, that's what was intended. They didn't want to hold ships from jumping if there isn't enough antimatter (especially given the number of antimatter-draining abilities), but they wanted quick repeated jumps to affect ships nonetheless. So now if you don't have "enough" for a jump it just takes whatever you have.

There are people that would hang you for this because they want the AI to stay and fight no matter what The way it works is the AI analyzes your fleet vs their fleet + modifiers (defenses, how important to them the planet is, etc) as a behind-the-scenes gauge on their chances. If the difference grows large enough, they retreat. Because so many people were complaining that they AI retreats too much, IC has been bumping up the allowable difference a bit in a few patches already. But ultimately it's a numbers game. It's possible that before you destroyed the capital, the AI was barely into the allowable margin

The infocards do update after research modifiers.. do you have a specific example? For display they are rounded, however, to the nearest whole so even though your 5% bonus on 10 points of damage will be calculated and do 10.5, the infocard might still show 10 since it rounds.

Edit: Not sure what's wrong with the formatting/font.. can't seem to change/fix it on edit

The actual value is used. The infocard information is just rounded to the nearest whole for easy display.