There is a difference between being well-known within the scientific community for providing analysis based on their clients' needs, versus being well-known within the public sphere for doing so. Yes, the LA Times reported on this pre-Deflategate, but it wasn't a big national story then, and firms could still get away with hiring a company like this. Now, sadly every football fan knows who they are, and most fans understand exactly how shoddy of a job these guys did (even if they hate the Pats and believe Brady was guilty, they look at the cell phone and not these guys).
Yes, the earnings drop wasn't caused by Brady accepting his suspension but rather, by the 5 cent earnings miss. Well, why did they miss earnings expectations by 5 cents? Because companies aren't hiring them because they know they are a liability in their field now. The NY Times puff piece pretty much states this with comments from the Exponent people themselves. They have their reputation to stand on -- and no one wants to be associated with a shady industry once their tactics are known to the public. Otherwise the NFL would be using Arthur Anderson as its auditors.