After thinking a lot about how to manage the thesis grades of our students, I have decided to use a course in Moodle. It seems as a natural choice since all our instructors and students have access to it.
To avoid confusion, I am planning to split students into groups depending on their advisor, what will allow faculty to see their tutees directly.
As a side effect, we get fast feedback to students and better visibility for administration. I am really looking forward to trying it.