At the moment, the extension doesn't checking category access when perform searching documents via search function. I can add code to check categories access level as well but it will causes the performance problem.
So the solution is that you set access level for individual document when add/edit document. Could you please do that ?
If you don't want to change access property for each document, you can get the file below, unzip it and upload to components/com_edocman/models folder. After that, when users search for documents, they can only see the documents belong to categories which they have access permission .