Given that one is still up and the other is not, I don’t think I am assuming anything about the reasoning behind the C&D’s. I’m a data-driven analyst at heart :).
At the time, a common belief was that jinteki.net’s online “gameplay” and/or use of the NRDB API and/or all deckbuilders were going down, i.e. that the two cases were related. However, no other deckbuilding sites were targeted, and jinteki.net is under active development, a sharp contrast to FFG’s unwillingness to work with NRDB at all. So it isn’t online gameplay (which NRDB didn’t have) or deckbuilding (which many places do) that was the issue. I’d think it was the api thing, but we know that NRDB offered to alter or remove that feature and that didn’t get anywhere.
I conclude, then, that there’s nothing other than coincidental timing indicating a relationship between the two cases. I haven’t seen the text of either C&D nor heard why jinteki.net was allowed to remain up; if we had that then obviously we’d know for sure.