It doesn't come up with an option to book from Chania to Heraklion on their web site so I would guess it is not a possibility? Also it is only a common route for a short time now, i.e. up to 18/12/2019.
I chose two arbitrary dates before 18/12/2019, looked at both the Piraeus - Heraklion route and the Piraeus - Chania route and they were the same ferry, i.e. Festos Palace, so it is clearly sailing Chania to Heraklion to Piraeus and Piraeus to Heraklion to Chania. I then looked at two identical dates in February and the Chania route was the Festos Palace while the Heraklion route was the Knossos Palace so they are then completely separate sailings.
Looking at the timings I would guess that just the sailing from Chania to Heraklion takes about 3 hours. I can drive from my house south west of Chania to Heraklion airport in exactly 2 hours. I would guess from Souda, which is already to the east of Chania, to Heraklion port, which is to the west of the airport, I could do it in around half the time of the sailing and that is not allowing for embarkation/disembarkation. It wouldn't be worth it even if it was possible.