In preparation for an interview he knew was coming Brady had a forensic examiner look at his phones before he destroyed the missing phone -- but he never gave that phone to the examiner. Then, on the day of the interview, he destroys the phone.
It makes no sense.
As for there not being "direct evidence," I think "direct" vs. "indirect" is a meaningless distinction. They have enough to support a conclusion that there probably was tampering going on, not absolute, but probable. They have enough to support a conclusion that it was probably that Brady knew about it. I think that's really all they need.