Those are two totally separate issues. The IG is not investigating whether or not there is a "deep state."
I have seen many different definitions as to what exactly is the deep state. To me, the deep state is not some vastly organized, secret government. Rather, I believe it exists in many forms. But in its purest sense, it's defined by some in power who operate for their own purposes, against the mandate required of their position. This can be career politicians operating in the interest of large donors, over the interests of the people who elect them. Judges legislating from the bench. And, it can be powerful people within various powerful government organizations who make decisions based on their own political, or financial interest.
No one trust politicians. Or, at least no one should trust them, so this comes as no surprise. If it turns out that this exists in the FBI, CIA or IRS that's a different story. That's a huge deal.
I still can't believe that James Clapper was ever allowed to head the CIA. He admittedly voted for a communist party candidate in 1980.