Hi!
In DA I got negative diplo "points" for starting wars, for exterminating a race and for breaking treaties (econ and/or research one I gave to AI). But differrent races had different "sensitvity" for the first two events.
You can avoid the first one with parking troop transport close to the race you want a war with, so they declare the war on you.
The second penality you avoid by getting peace treaty just before the race is exterminated. E.g. you don't take that race's last small planet, and make peace treaty with it. When that planet flips or the race surrenders, it's not counted as you'd conquered it.
The third penality you avoid by not giving your econ and research treaty to anybody. I usually saved the research one for the most hostile and strong neighbour, so I'd got one diplo plus with it. Coupled with one trade route and better diplo ability it was usually enough to avoid being attacked by that race, this develping my empire in peace for another game year or more.
Does the A.I. also get diplomacy hits for conquering planets?
AIs play (mostly) by the same rules as the live player. So penalities I counted above very likely apply also to them.
BR, Iztok