I think it is just mostly Lore for the reason they are separate, along with the expansion locations and currencies involved also.
The ARR hunts are offered by The Grand Companies and use Allied Seals currency, the HW and SB hunts are offered by the Clan Hunt - Centurio and use Centurio Seals, ShB is Clan Nutsy with A Sack Of Nuts currency, and EW is via the Gleaners Guild under Guildship Hunt using the same currency as Nutsy.
Although, I do find it strange lore-wise that Nutsy and Guildship use the same currency, even though its different planets :P

That said, It would be kinda nice to have a House of Spender's style universal board in main cities, to just use to get Hunt Bills.