Although, as 2DT says, wind turbines are common in anime, they are not common enough for us to deduce common themes. I would say for now they simply work on case-by-case basis. In Shangri-la, they are definitely a part of the enviro kitsch. In Haibane Renmei, maybe not so much.

Note that Haibane Renmei was filmed before the turbines dotted the contryside.

For the image of the turbines to work, they have to tap into a stereotype. At the levels they are used in America, wind turbines add to CO2 production, not detract (it's because due to variability in wind power, and the absolute requirement to balance the grid, backup power plants must be kept on standby, mostly coal-fired). It may or may not be the case in Japan. However, using Dr. Goebbels' first principle[1], the mega-machine of media created an image of "eco" for the wind turbines. Naturally most anime would want to tap into it.

Not necessarily all though. I do not have a turbine example, but the way J2 mocked Global Warming (before the Climategate!) was very illustrative. Creators with conscience feel intuitively when they are being brainwashed, and some are compelled to speak out -- if not against the cause, but against the instrument.

P.S. Forgot one funny tidbit: I drove by Altamont many times and once I saw a turbine starting a decent grass fire. Apparently it seized suddenly and the momentum of the rotor was enough to rip out the fasteners of the generator. When the hot generator fell to the ground, it started the fire.

[1] Joseph Goebbels formulated and applied two bedrock principles of mass-media propaganda: 1) people will believe any lie if repeated incessantly, 2) lie must be so incredible that people would not believe into a possibility of such lie and accept it as truth.