Pathfinder Online's Lee Hammock explains in today's most recent blog post that it can make a huge difference.
First off, the type of hex matters. Whether it's a settlement hex, a wilderness hex, a monster hex, or an NPC hex, each version determines control capabilities, building laws, resources, and so on. This basically means that no two settlements will be alike.
If you'd like to read up on how much territory and the hex map actually matters in Pathfinder Online, head on over to the dev blog to read more.
[Thanks matixzun for the tip!]