In addition I would be a bit surprised if wine has copied 11000 lines of header files from windows, arranged identically to Microsoft Windows source code.
It seems you are arguing mainly because the user base is so much smaller it does not count. The law does not work that way.
Windows SDK contains tens of thousands of lines in header files for those DLLs Wine implements. Not saying Wine copied them outright, but the opportunity is clearly there.
It would be up to Microsoft to demonstrate that Wine impact the market for Windows license sales. I strongly doubt they can do that regardless how much they have spent on documentation and developer tools. Wine does not replace the need for an operative system, and if the usage ever become widespread enough to harm the market for windows then developers would just support programs natively for Linux, side stepping the need for wine.
Wine is not a market substitute for Microsoft windows, which is the first consideration that courts look at. Courts would then look if there is a potential existence of a licensing market (ie Microsoft licensing out the ABI) which again does not seems very likely. Failing those two tests it would be a rather uphill battle for Microsoft to demonstrate Wine impact on the market for Windows license sales.
Copyright law needs to be clarified to allow this without licence. Just like you're allowed to refer to a competitor's brand if you follow the rules in trademark law. It's one of those things where you think legislation should be rushing to fix it to remove uncertainty. Instead, a good chunk of senators is comfortable letting the Ellisons of this world make other people's life harder in negative-sum games.