Gamers Nexus launched an investigation and compared four Taiwan-made fans with four China-made fans. The site reports that there are indeed some minor design differences between the fans, which can be a bit of a problem if you want to color match fans. But there's no difference in performance so the pitchforks can be safely locked up in the shed again:
Companies change supply and factories all the time. People notice differences all the time, too. The only change here is that Noctua was noticed (doing something mundane and uneventful) and, for whatever reason, the PC hardware community latched onto it for lack of things at which to direct pitchforks. Cooler Master changes the fan used with its oft recommended Hyper 212 – and those differences are far greater than these. NAND supply changes. DRAM supply changes. Even the switches used in mice change. Ultimately, all that matters is that the product matches the spec that it has always advertised; if it does, then no big deal.