Regardless of the master's or doctor's degree, there is usually a page of authorization in the graduation thesis, asking the author to authorize the university to use the thesis. Therefore, if HowNet is not authorized by the author of the paper and the university itself does not cooperate with HowNet, then the doctoral thesis of the university will not be uploaded to HowNet for public.
HowNet is an enterprise, not a state department, and there is no possibility of compulsory acquisition of university dissertations. This transaction must be voluntary by both parties, and whether to upload HowNet is the independent choice of colleges and universities.
Some universities have their own databases of academic papers. For example, Wanfang Database was built by Peking University itself, so naturally it seldom uploads papers to Tsinghua-controlled China HowNet.