Considering that it sank like 2000 years ago, would there be any detectable molecular traces left to figure out amphoras’ contents? Or would everything be destroyed by now?
It is possible some of the containers are still sealed. It does sometimes happen. I am looking forward to hearing if that occurs (and if the contents are "intact"). Mmmmm...2000 yr-old fish oil!
Yes. Amphorae commonly held agricultural products for trade, like grains, oils, wine, herbs etc. They've got some good molecular techniques going these days for analysing remnants.