Honestly, that actually makes sense. A hive mind has no real government structure, just itself. A non-connected species that is ruled by the hive will need to have its own government structure under the hive, even if its people were completely integrated in the hive civilization. And without access to the hive's own network, participating in the economy directly would be very tough. Enclaves only make sense at that point.
I'm not really sure I follow this, why non politically active pops in a hive mind need their own governing structure especially compared to say, non politically active pops in some other autocratic society. The economy question is more interesting, but it's hardly an impossible question to answer, whether it ranges from some communistic arrangement (along with possibly a black or grey market that runs without the hiveminds involvement) to the building of an economy within the empire to accommodate the pops (especially in a xenophile style hivemind with many, maybe even most, of their pops being non hive mind aliens). The answer to these questions could be some very cool content even, as your hivemind first meets and then must come to decisions on how to deal with populations of sentient non hive mind creatures. "Purge them." and "Make them into separate vassal states" are both valid options, but they are not the only (Logical, gameplay wise they seems to be) ones.