A Nintendo representative named David Marshall stated the below:
“A unified account system will be implemented later this year with the launch of the Wii U. Eventually this same account system will be made compatible with Nintendo 3DS systems. At this time we have no additional details to offer and nothing to indicate how or if this will work outside the United States and Canada. In the meantime, if the system has a problem, taking it to an Authorized Service Center will maintain the Nintendo eShop account. If the system is stolen, we can transfer the account to a new system once we are provided with a valid police report.”
Marshall here brings out that Nintendo is going to implement a unified eShop account system that you will be able to use at the time of the Wii U launch. He also stated that this account system will also be brought over to the 3DS, so it looks like you will be able to have one account that connects to your 3DS and Wii U. Plus, if your system somehow gets stolen, Nintendo will be able to transfer your account to another system.