This is because:
* On-set details are kept confidential. Production companies and actors are very careful about revealing private information about filming, particularly intimate scenes.
* Filming can be staged in various ways. Actors may film a scene in different takes, with different levels of intimacy, and the final version may be edited to create the desired effect.
Therefore, any answer about their specific clothing would be speculation. However, it's highly likely they were wearing clothes, as it's standard practice for actors to be fully clothed during filming, even for intimate scenes. The final scene in the movie is edited to appear as if Harry and Hermione are sharing a kiss, but it's not explicitly shown.
It's important to remember that actors are professionals who understand the boundaries of their work and are committed to delivering the best performance possible while maintaining respect for themselves and their colleagues.