If you want to do individual encounter lists for each hex just make sure they're all the same size and can be rolled with one die. So seven d8, d10, or d12 lists. That way GMs can still run it smoothly and not have to check what die to use across the hexflower.
That said, try to do a single 20-entry list. The encounters are for events that happen while the party's wandering the map outside of the special locations, and hexes are big. A 6-mile hex is a little over 23 square miles of territory, the dungeon/town/other locations won't take up the whole space.