Only if the resources lost due to piracy make it into the Arrgh Bank
I do agree with the sentiment though, Alliance trading should be used more often. Cyber Nations did this by giving you a happiness bonus when you traded with people in the same colour team as you. I dont believe resources should be "lost" however, I think there should be like a 2% commerce bonus for trading with your own team that lasts 3 days, but it doesnt stack, just a new trade with your color resets the timer.