Forget the wake by avoiding it altogether
The idea of having a huge, hollow ship is unrealistic even in a fantasy setting. Aircraft carriers are made out of steel and not English Oak because ships that size require the advantages of steel and mighty engines to exist. You didn't say whether or not your ships are made of steel or depend on combustion.
So let's assume your fantasy setting is akin to the Golden Age of Sail. Your hunters are, I assume, fast short-range ships. It's implausible (frankly unbelievable) that your carrier would have dock or bay doors that would open to let them exit and enter. To do so would require a power source other than wind and sail.
I recommend long, skinny, and cranes
Let's assume a very long, quite skinny ship that has cranes along both sides of the ship for lifting the hunters out of the water. This not only provides access for repair and resupply, but keeps the hunters out of the water to reduce drag, holding back the carrier. Cross-beams could be moved into position to lock the hunter in place, which would have the advantage of adding the hunter's sails to the overall propulsion of the carrier.
A pair of cranes mid-ship have the unique ability to lift up-and-over, thereby bringing very damaged hunters into an onboard dry dock for extensive refit.
The long carrier would have the advantage of speed due to a minimum water cross-section, which would also allow for a lot of keel-aligned sails, but would have the disadvantage of turning a bit like a lead brick. Good! There should be disadvantages to outweigh the advantages.
An average carrier might host eight hunters with cargo capacity to allow for 3-7 year patrols. Do I have any stats to support that? Nope. It just feels believable to me.
But what about that darn wake?
Since the hunters are always working along side the carrier and never behind it, the wake is a non-issue.
Post edits answer
The OP has since edited his/her question to indicate the ships are made of metal and have powered engines.
In this case, I don't advocate a carrier. I advocate tethers. All the hunters can move under their own power so long as supplies and fuel are available. This minimizes the size of the carrier and improves both its defense and its economy. Rather than being a huge, lumbering clunker when the hunters are deployed, it's a small supply ship... fast and maneuverable. A single "bay" at the back (not actually covered, but a forked portion of the stern) would exist where a hunter can be brought in and parked for repair and maintenance.
Curiously, this reflects an answer I gave to Optimum Shape for a Space Dreadnought.