@Timeshift: Let's see...
I won't assume that the lighthouse town is Water or Electric--after all, Olivine City has a lighthouse, and Jasmine is a Steel-type leader. Perhaps the same is true in Isshu? Regardless of the lighthouse, though, the nearby castle seems almost too conspicuous
not to be a gym. That would leave three more gyms, one of which is in Sekka.
Scans from back in June seemed to allude to the beehive structure being located in the northwest forest, as you suggested. (Never mind that they mistakenly took it to be a blast furnace, the honey being mistaken for molten rock.) However, take a look at this picture of the in-game map:
It seems that the large yellow circles are major cities/locations, i.e. those to which the player can fly. If we go with the convention that gyms are only located in places accessible with Fly, then I would wager that the structure in the northwest forest isn't a gym. Likewise, I think the cliffside in the north is Victory Road, and the plateau is the Pokémon League. That leaves six (6) "available" dots on the map and three (3) gyms. We know Sekka City Gym is the northwest dot, which leaves:
* Lighthouse town west of red bridge
* Airfield town west of mountains
* Dual-dragon town north of High Link
And the three yellow dots surrounding the eastern mountains, all of which are shrouded in clouds on other maps of Isshu. Since it seems that the player travels clockwise around the circle from Raimon City, I would guess that Sekka City is actually sixth in line, with the other two gyms being somewhere beyond around the circle. Or, perhaps, Sekka City is actually the fifth gym. I think the dual-dragon town is almost certain to have a gym, so that would leave the other two gyms to be somewhere along the eastern mountains.
Other points of note:
* Dragon Spiral Tower - castle north of Sekka City
* Tower of Heaven (presumably) - spiral tower north of airfield town
Tentative list:
1) Sanyou City - Dento (Grass)
2) Shippou City - Aloe (Rock?)
3) Hiun City - ? (Flying?)
4) Raimon City - ? (Electric?)
5) (Lighthouse town) - ? (Steel?)
6) Sekka City - ? (Ice?)
7) (Dual-dragon town) - ? (Dragon?)
8) (One of three eastern mountain towns) - ? (?)
I'm kind of hoping that we do away with type-themed gyms at this point, but I guess time will tell.