Hello Kyriakos Papadimos,
Thanks for reaching out. Updating the fields/columns (of type Managed metadata / taxonomy terms) of a list item in a SharePoint document library is not possible using Graph API. Please refer to the Graph API GitHub form page for more information: https://github.com/microsoftgraph/microsoft-graph-docs/issues/4911. I would suggest posting your query and feedback on the Graph Feedback Forum.
If the reply is helpful, please click Accept Answer and kindly upvote it. If you have additional questions about this answer, please click Comment.
Thanks.