I mostly agree with you in your response to the second point. I don't personally find as much fault with the readability issues because the logo would pretty much always be seen in the context required to make it decipherable, but I can understand why one might take issue with that. Ultimately, its important to remember that the logo is neither the brand nor a stand alone work of art. It is only a part of a system.
I think ultimately the pitfall of the don't make me think school of design is that it is susceptible to joyless, by the numbers design but I understand its utility. Also, ironically, one could probably say the same thing about modernist design.
Your article brings up some interesting points and valid criticisms, but I just don't personally agree with all of your values when it comes to design.