When a government makes a court secret, I tend to infer the worst interpretation of the activities they're hiding from us. We have no means of checking whether the FBI is putting any care into their warrant applications. We have no way of knowing if the judges even read the affidavits, or what level of scrutiny they apply to the requests, etc.

All we know is that they grant 99.98% of the warrants asked-for. That's a massively suspicious rate of approval that is more likely explained by the rubber stamp than careful consideration and evaluation.

Nothing in this world has that kind of success rate without some sort of shenanigans.