Could be that Cooper, without wishing to broadcast it to other teams, just wanted to rest Roberts whose all-action displays must be taking a toll. If anything, Nauts is probably the better defender and Cooper probably thought that was no bad thing given Barnsley's style of playing. And, being fair, Nauts didn't disappoint putting in a really sound display with the rest of the defence yet still finding time to set up Ayew for our goal..
Granted Roberts is a far better attacker as you say but Cooper set his stall to defend and counter which would not have been my choice either. However, his decision was vindicated by the 1-0 lead we take back to the Liberty and he will be further vindicated if we defend or increase our lead. But I hope we do it playing some football this time.