(A) had discovered 17 nearby stars that are orbited by planets ----> Correct - Past Perfect is correctly used for 2 related non concurrent events.
(B) had discovered 17 nearby stars with planets orbiting them that were ----> 'that were' indicates that the stars were of the size of Jupiter in the past and are not of that size now.
(C) had discovered that there were 17 nearby stars that were orbited by planets ----> 'were 17 nearby stars that were orbited by planets' indicates that the existnce
...
(B) had discovered 17 nearby stars with planets orbiting them that were ----> 'that were' indicates that the stars were of the size of Jupiter in the past and are not of that size now.
(C) had discovered that there were 17 nearby stars that were orbited by planets ----> 'were 17 nearby stars that were orbited by planets' indicates that the existnce
...
