The reason why Surah Tawbah does not have Bismillah in the beginning is that there was a possibility of Surah Tawbah being part of Surah Anfaal (Surah before Surah Tawbah) and not being a Surah on its own. So, writing Bismillah here will be incorrect because (if Surah Tawbah is in actual fact part of Surah Anfaal), then it will be as though a person is writing Bismillah in the middle of a Surah.
Another reason is reported by Sayyiduna Ali (Radhiallaahu Anhu), ?The reason for Bismillah not being written in the beginning of Surah Tawbah is that Bismillah indicate towards peace, and the pact and peace treaty with the disbelievers was terminated by this Surah. (so it was not appropriate for Bismillah to be written). (Ma?ariful Qur’aan vol.4 pg.307; Idaaratul Ma?arif, Karachi)
and Allah Ta’ala Knows Best
Mufti Ebrahim Desai