A spell or ability that counters spells can still target Akroma. When that spell or ability resolves, Akroma won't be countered, but any additional effects of the countering spell or ability will still happen.

If Akroma, Angel of Fury is cast face down, it can be countered.

In a Commander game where Akroma is your commander, you may cast it face down from the command zone by paying {3} plus {2} for each time it has been cast from your command zone. The cost to turn it face up is unaffected. While face down, the combat damage it deals is still counted as damage dealt by your commander.