Hey @Mathieu - and welcome to the community! As you know, Monday is infinitely flexible! This gives the platform so many benefits but at the same time, its forever flexibility can be a detriment (depending how you look at it! )
How you setup your Workspaces is a lot of personal preference, however it really boils down to organization, continuity and security and what your overall goals for Monday.com are.
Depending on the size of the operation, we do recommend splitting things out by department. This gives an easier way to organize your security if only members of a specific department should have access to the boards and visuals within. This also allows for groups to have their own spaces and develop their own board designs etc. Additionally, it keeps the views clean for everyone involved. Everything in a single workspace begins to get a little crazy with departmental requirements.
You should also keep continuity in mind. If there is a goal to take data from multiple areas, summarize and report, ensuring you have proper templates setup is key. This will make your life much easier down the road.
Hope this helps! And feel free to reach out at any time.