correct me if i'm wrong but shouldn't defending deeper mean that you are less vulnerable to the counter?
If the whole defence (ie not just the 2 cb's like in our case) and the midfield are adjusted and rerady to break their necks to get back then yes.
However when the two full backs are out wide (probably standing static) and we lose the ball, are wafer thin midfield are nowhere to be seen, this is when the two centre backs should step in and close the space down, but they don't, they back off, the ball is played in the space between them and the fullback and we're fucked, any team with a decent manager would see this and exploit it, which Reading did.