Are you solely concerned with Chania or Heraklion?
We will be going to Heraklion in October, as we always do, and I am hoping that as it is a relatively quiet time of year, there will be little delay. I suspect the press is looking at mass tourism destinations, at peak season, with many flights from the UK and outside Schengen areas, where there will inevitably be delays due to the greater number of tourists. The smaller, quieter airports shouldn't be too bad.
We landed in Mytiline (Lesvos) in June this year, and did notice that the passport check was properly thorough, you had to hand the passport to the border guard, and details were entered/checked on their computer, something that has rarely happened in the recent past, so there was a small delay, but as Mytiline gets so few UK flights ( 2 a week this year!!) I don't thing it will ever be a problem there, nor at Kalamata airport, where we also go each year, and is smaller still than Mytiline.
Leaving Greece posed no extra problems, just waved through!
Heraklion can be a nightmare at busy times, so lets hope any extra security won't make it worse, never had the pleasure of flying in to Chania, but views expressed here on the forum suggest it is a nicer experience than Heraklion.
P.S. only 10 weeks to go to Plakias!!!!!