Be struck that is an unfamiliar phrase to me. Is it a standard English?
Reading Principia by Newton, John Locke was struck that generations of philosophers had been so preoccupied with their own comprehensive metaphysical systems that they failed to be open to the lessons of experience.
Yes it is standard, though not as common nowadays as it was in the late 19th and early 20th centuries. As an example "It struck me that consistent printing is important for speed reading" means I suddenly realised that fact. "It hit me that" is similar. "It occurred to me that" is similar but weaker. Often the importance of he fact is recognised as well. In your example John Locke suddenly realised the truth and importance of the fact that ...
The verb strike has a lot of meanings. In this case it means "to discover", or "to realize". So the sentence means:
Reading Principia by Newton, John Locke realized that generations of philosophers had been so preoccupied with their own comprehensive metaphysical systems that they failed to be open to the lessons of experience.
