Could be related to two issues:
1. technical - gren decreased armor value
2. gameplay - soviet and german inf squads are more static now, due to the fact they need to stay in cover and not moving so much as before. Mortars are less accurate on moving squads.
Armor value never had an influence on explosive damage, only on small arms fire. The old 1.5 armor grenadiers, 2.25 armor shock troopers and 1 armor conscripts, all took the same damage from explosives.
Your other point is probably why the mortars seem better now. As far as I know the mortars did not receive a buff.
I don't think cover ever mattered to aoe weapons. However, units clumped up in cover well be easier to take out with aoe weapons.
I've seen chest-high walls protecting units from grenades/mortars landing on the other side. And some craters also seem to protect the units hiding inside of them. Cover does help when it's between the units and the explosion.
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