Actually there's a huge difference.
If you attach the disk to an AP base station your transfer speeds will be limited bu the CPU in the base station doing the routing and that chip's really slow (like in all consumer NAS). You will be lucky to see more than 3 MB/s.
If you attach the disk to another Mac and share via AFP you will be mainly limited by the network and in case it's a Gigabit connection by the disk itself. On an 802.11n network you should see ~8MB/s, on Fast Ethernet a bit more, and up to ~90MB/s on Gigabit if your disk is actually that fast.
The only advantage to doing it via the base station is that you don't need to have another computer running all the time to access the disk. Attaching the disk to the AP BS is convenient. But if you are worried about performance you should always opt for attaching the disk to a real computer rather than a slow NAS box.