DuckDuckGo is not owned or controlled by Microsoft. Microsoft isn't even an investor in DDG. DDG uses Microsoft search and ad network services, receiving compensation in the same way that many websites and individuals, including MacRumors, do from companies such as Amazon, Microsoft, and Google as affiliate partners. That doesn't mean DDG is controlled from Redmond.
Aside from the fact that ownership or control by a company is very different from being a client or customer of a company, it is easy to look at MSFT's quarterly and annual financial reporting and see that DDG is not part of MSFT's corporate structure. As an extremely high visibility global company with a widely held stock, pretty much everything MSFT does that is of any consequence becomes publicly known, either from MSFT itself or from stock analysts and media outlets. Plus in the political environment that has been in place since DDG's launch, any move by MSFT to acquire DDG would create a lot of antitrust publicity.