The clan level 3 perk is 10% extra loot from wars. Does this apply on the war that levels your clan up or does it come into effect the war after the level up?
The way clan perks work is a bit like 'WYSIWYG' (What You See Is What You Get); what I mean by that is that the 10% extra bonus loot is added in the figures you will see in wars. I'll explain:
When you are in a war and check a base from the opponent side, you see how much war loot this base is worth. At clan level 2, let's say that you see 300,000 gold (usually standard early/mid TH8 base). This is exactly the loot you will get if you win the war, regardless of whether your clan level ups or not.
At clan level 3, you would have actually seen 330,000 gold on the same base (the 10% already incorporated in the figures).
So to answer your question, clan perks apply after the war that clan won enough exp to level up.
I just got this as well, It takes effect in every war after you achieve that Level.
Example. I am in a current war with Clan Lv.2, at the end of the war I receive 400,000 Gold & Elixer and my clan levels up, I don't get the 10% of my 400K gold & Elixer added onto it. But next war 10% more loot will be available for me.
Hope that helps :)