The only strikes that have affected air travel have hit all Greek airports, because the Air Traffic Controllers came out. There is one ATC centre in Athens that covers the whole country. ATH has had more problems with ground transportation than the regional airports, but if you're only changing flights that won't be a problem.
Some of the sites that show flight movements don't get an update from the Greek regional airports, so it looks as if things are normal when in fact nothing is moving. Try looking for the flight at the other end of its journey and you'll see cancellations or delays until the strike is over.