I'd say it was because the game let him age a bit. Having a body double makes no sense at all in the context. The Emperor did it because he knew he was going to be killed. Your contractor believes you're bound by the sacrament, and indeed when you kill him, he says "We had a deal" as his dying breath. He had no expectation that you would turn on him.
Really? Let him age a bit? That's the best you've got? What is there to age? Something tells me people aren't exactly taking this quest and then waiting several years in-game before taking it on again. Come on man, the two Motierres look nothing alike. See for yourself:
The Motierre we meet in Volunruud: http://oyster.ignimgs.com/mediawiki/wiki-api.ign.com/the-elder-scrolls-5-skyrim/thumb/5/5d/NPC_Amaund.jpg/468px-NPC_Amaund.jpg
The Motierre we meet in Whiterun: http://skyrimming.com/wp-content/uploads/2011/11/600px-SR-npc-Amaund_Motierre.jpg
There's also several other things to pay attention to that make me strongly believe the second one is a body double, aside from the obviously different facial structure and features.
1. While a whiny, snobby and spoiled brat, Amaund Motierre is highly intelligent and capable. He himself formulates and puts into action a multi-layered plan that opens up the Emperor as a target. He is intelligent and knows how to cover his tracks and tie up loose ends.
2. In Volunruud, Rexus is there with him in case things go sour. In Whiterun however, Rexus is in an entirely different room. For a faithful servant who supposedly never leaves Amaund's side, it was most peculiar to notice...
3. Amaund Motierre is a descendant/distant relative of Francois Motierre, a Dark Brotherhood contract from Oblivion. He knows who he is dealing with, and so is very cautious as a result.
4. If Amaund has "aged a bit" as you profess, then why hasn't Rexus who is supposedly with him at all times?
5. When I asked Babette about the contract, she says "The man you need to speak with, his name is Motierre? That's a very old and powerful Breton family, firmly established in Cyrodiil. Most curious..."
There is simply too much about this guy and the situation that doesn't add up, and "he aged a bit" is definitely not the answer. Amaund Motierre still lives.