What does "I worship the Lord of the Thunderbolt" mean, in a translation of Shantideva's Bodhicaryavatara?
I would think it refers to the author's main Vajrayana teacher. As ChrisW rightly notes: Thunderbolt is a translation of Vajra. the lord The student-teacher relationship is very important in Buddhist tantra and Santideva was an Indian practitioner of Buddhist tantra. 

There are several reasons to think that it refers to his personal teacher:
1) in tantra one is supposed to see the teacher as one with the highest Buddha 
2) in the text here it says that the author has neglected 'his instructions' - that is, the instructions of the Lord of the Thunderbolt. That makes most sense if it does refer to his personal teacher.