1. It's a constant penalty that grows smaller over time. Both participants in the war get the reputation penalty every turn until the war is over. And yes the bonus/turn for alliances is twice than that of the penalty/turn for being at war. Keep in mind depending on when each alliance/war was started, the diminishing returns for either might make one very small versus the other (for instance if you've been at war for a very long time, the penalty will be pretty small, but if you allied two turns ago, the bonus/turn is fairly high). Short answer: But you're correct in that an alliance cancels two wars if both happen at the same time.
2. I don't believe so. Least it'd be crazy to think that CA would code in a continual penalty for being at war with a destroyed faction. Short answer: I think after you destory a faction, you're considered at peace with that faction.
3. Attacking itself (assuming you're at war already) doesn't affect reputation, only relations with the faction you're attacking. Attacking an ally of your ally hurts relations with both your ally and the 'victim.' Attacking the enemy of your ally, hurts the relations with the enemy/victim, but boosts relations with your ally.
Short answer: Yes, releasing and executing only affect reputation of the actions you've listed.
4. I don't think you get a penalty for being at war with a dead nation so this shouldn't matter.
Yes, it does raise your reputation, mainly because you're adding another 'alliance' to your faction and stops a war you were having. It also affects the vassal's reputation since it generally adds an alliance and stops any wars they were having with you and your own allies.
Hope that helps and if you're still confused, don't worry. I enjoy talking about this stuff. You might even find out something I don't know (ie there might be code that gives a penalty with a dead faction after all, I've just never heard of it or seen its repurcusions in game.)






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