You could really go two ways with a redesign of the Reef.
One is the mobile stealth/rearm idea (which I think would necessitate a reduction in cost and size by a lot, unless it rearmed much faster) (It has 175 worth of airpad and it would have 600 worth of area cloak.)
The other is to commit to the drone idea, but switch the drones to being the D-ability, with limited duration deployment. Instead of continuously building drones to replace the lost ones, it instead "stockpiles" (no metal cost) drones and launches those when ordered. After 30 seconds or so, the drones automatically return to the carrier and dock, vanishing from sight. Both the D-gun recharge and restocking of drones is paused while drones are deployed, making them a bit less spammable.
At the same time it would make their strike power a bit more resilient against being in AA (and also means that Reefs no longer die if there's enemy AA on the port side.)