Sorry Chrissyg but we don't have a crystal ball. Shop opening is determined by the government and I only have a vague idea of what the government rules are now let alone what they will be a couple of weeks from now. All I can tell you is that large supermarkets aren't open on a Sunday now. If they will open, when they will open or what hours they will open is unknown.
At the moment supermarkets are open 08:00 to 20:30 Monday to Saturday. I presume that is because of curfew. Normally from about 1 May they open up to 21:00 so if curfew ends soon I would expect them to return to that schedule. If by "open late" you mean after 21:00 then no, I would not expect them to be open. I have never shopped on a Sunday so even if they do return to Sunday opening I don't know if that also goes up to 21:00.
The nearest Synka to Heraklion airport is on the road to Knossos quite close to the junction with the new national road. Their contact details are:
You could try contacting them directly closer to your departure. Mini markets can do whatever they want once curfew is lifted. I know one on the Omalos road close to the junction with the new national highway that is normally open pretty much 24 hours per day so I tend to use that if I am returning from Chania airport late at night. I am sure there must be something near your route. You don't say which direction you are going. If you are heading east I would expect there to be something open in Herssonisos or Malia. If you are heading west then there is very little so you might be better to head into Heraklion before getting on the national highway.
That is what has been said by Development & Investments Minister, Adonis Georgiadis, in an interview on Skai TV on Sunday, Mixos, but there hasn't been an official announcement of that yet as far as I know. The government has a bit of a track record of ministers saying what they want to happen and then it not happening. The Tourist Minister and the Development & Investments Minister are both desperate to get things open. Others, like the Protection Minister, are more cautious. I would expect an official announcement some time this week.