Well, my 20GB model (bought a few months after launch) is the HG01 type.
I would guess that they could be transitioning to the HH01, but in the meantime using up the existing HG01 cases. I don't know why they're laid out differently, but it's probably something internal. Maybe they got better cooling results, or maybe it's just easier/cheaper to produce them in the new configuration.
The HH01 may have been used because it was better for vertical orientation (since the connections are lower), but they may have found that many people don't have their systems vertically oriented. I know it's only anecdotal, but most pictures I've seen of people's setups have the PS3 horizontal.