I get what you're saying, but there are a couple issues with that argument. I think we can be about 99% sure at this point Nintendo doesn't track what LFCS is linked to what console. There also seems to be reports of people having incomplete system transfers and ending up with the same LFCS on both systems, so there probably are a lot of legitimate customers that are unknowingly using a LFCS shared between a couple systems.
Take the above with a grain salt, of course.
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Your Wii U purchases should be fine, but I personally would avoid purchasing anything on a NNID associated with pirate activity.
You won't be able to link a new or different NNID doing just this tutorial, but there is hope for the future that this may be fixable, eventually.
What error are you getting with SMM? Nothing in this tutorial would effect the installation of games.