She also winces and jumps when Harry uses his name.
When Hermione meets Harry for the first time in Chapter Six of Philosopher's Stone, she tells him:
I know all about you, of course -- I got a few extra books for background reading, and you're in Modern Magical History and The Rise and Fall of the Dark Arts and Great Wizarding Events of the Twentieth Century.
If she knows about Harry from reading those books, then logically she'd also know all about Voldemort, his reign of terror, and the taboo surrounding his name. Hermione's a very compassionate person, and it makes sense to me that she'd join in with the taboo to avoid upsetting or offending anyone.