I remember when the zones were first introduced - early 80s from memory - and a bloke from London Transport was discussing it on the TV. It mattered to me because it was about the time I started travelling into London.
He said that the Zone 1 was supposed to cover the area between BR's terminal stations - essentially the area inside the Circle Line, Northern Line between Euston and Moorgate, and down to London Bridge. (I think Borough and Aldgate East being in Zone 1 were exceptions to this, as they are today.)
There was a significant premium for using Zone 1. The reasoning was that the main terminals and tube lines in between were congested whereas further out there was free capacity. He said it was the same logic as offering cheaper fares after 9.30am or at weekends.
Based on the original logic, Shoreditch High Street probably "should" be in Zone 2. However, even if the original logic was indeed to disincentivise people from using Zone 1, or at least make them pay the price for doing so, with the Overground opening offering through commuting journeys so close to the centre, then as noted earlier, the revenue "loss" would be too great. Hence Zone 1.