There are three options. You've touched on at least two of them.
1. Indirect Area Combat Spells don't allow a defense test, therefore Counterspelling does not give any bonus.
2. Counterspelling can be attempted, you roll just the dice used up from your Spell Defense pool. Hits achieved effectively reduce hits on the spellcasting.
3. Spell Defense Dice can be applied to those that are hit by the spell, those dice apply to the resistance pool.
Personally, I like to go with Option 2, it makes things more dynamic and increases the chances that spells might deviate or do something more "interesting".