As of 7 April 2019, the Hellenic Police will begin implementing systematic passport control checks for all European citizens travelling to/from destinations outside the Schengen area (including the UK). This is in line with the 2017 Schengen Borders Code regulation EU 2017/458, which will eventually be applied by all Schengen member states according to the individual timescales. Waiting times at passport control may be affected on departure from and arrival into Greece. You should ensure you arrive at the airport in good time.
This is nothing to do with Brexit its because we are outside the Schengen Area - its only advice and starts tomorrow. If you do suffer delays then please tell us, i am thinking it may be that all passports will be checked through the computer as they are on return to the UK.