I'm sure there is a "deep state" of bureaucrats somewhere, but the temptation is to use it as a general catch-all to deflect culpability from failing politicians.  White House leaks are not a sign of the "deep state" but rather of incompetent leadership (Bush was a Republican goon and didn't dwell in a sieve), and Trump's issues with the Senate are similarly nothing to do with the "deep state".  

It does make for a convenient explanation, and is I suppose about as sophisticated an explanation as the Trump sycophants are capable of processing, but ultimately, it's just a bunch of bureaucrats doing what they do and what they've always done. The President is not king.