That seems to be the case as revealed by a Nintendo customer service rep David Marshall. This email exchange can be read entirely 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.
Keep in mind that this is still considered a rumor until someone higher up in the Nintendo food chain confirms it.
Nevertheless, if true, this would be a very welcome change in “modernizing” Nintendo’s digital platforms.