“Many sons of talmidei chachamim have been ballei battim.”
Apparently, Rav Shach felt a need to explain why his son turned out this way, since he didn’t feel it should have happened.
By the way, though, Joseph didn’t say the issue was that he wasn’t a baal habas. He said the issue was that he wasn’t a big Talmid Chacham (which isn’t necessarily the same thing).
Personally, the way I heard the story was that he was upset that his son didn’t take the same path as him – meaning that he had a different hashkafa. This doesn’t necessarily contradict what Joseph wrote since part of having a different hashkafa could include not being a Talmid Chacham, but it does explain why it was unexpected.