Question: At what point does Will actually realise that Thomas Kent is really Viola?
Answer: When they are in the boat, just after "Thomas Kent" delivered Viola's farewell letter to Shakespeare. After a brief discussion about Will's feeling's for Viola, Thomas (Viola) kisses a surprised Will Shakespeare, then rushes away when the boat docks. The ferryman comments to Will that it was actually Lady Viola.
Question: How did Will not recognise Viloa in her boy disguise? Even in disguise, you can clearly see it's her, and she didn't sound like a boy.
Answer: In real life, Viola, of course, would be recognized as a female in disguise. However, in literature, film, opera, etc, it often is necessary to employ what is known as a "suspension of disbelief." That is, the author expects the reader or audience to know something is impossible, unlikely, or completely unreal, but they have to accept a certain premise in order to allow the plot to unfold. We go along with the idea that no one realizes Viola is actually a woman, so that we can enjoy the overall story.
Question: The scene when Wessex thinks that Shakespeare is dead, but he then comes into the church and Wessex thinks he is a ghost come to haunt him, seems like the scene in Shakespeare's play Macbeth when Macbeth sees Banquo's ghost. Is this another example by the film-makers of showing how Shakespeare's life inspired his plays, or just a coincidence? Was Macbeth written before or after this film was set? Thanks.
Answer: Oh, it's undoubtedly intentional, another of the many nods to Shakespeare's work scattered throughout the film. The precise date of authorship of Macbeth is unclear, but even the earliest likely date is still some years after the setting of the film.