Things definitely do despawn. I suppose if you leave the area quickly so that the area goes inactive, and come back later it might still be there, but I was working a crypt the other day, went back to my base to work the first load of iron ore, and all the items in the water, including iron ore, had despawned. The base was a reasonable distance away (well out of render distance), and I was there for 2-3 days.