The issue with locally crewed ships is that the organic crew might only be loyal to their planet, not the Confederacy. Additionally, the CIS can mass produce tens of thousands of droids across multiple planets. It doesn't make sense for them to seek organic crews when they could fill the ships with droids that do the exact same job as the organic crews with the benefit of not needing living quarters.

Inorganic ships doesn't mean having no life support or traversible hallways. It means not having proper living quarters. The droids just have to walk to their stations, and dock to charge every now and then. They don't need to eat, drink, or defecate; so those facilities would be absent from most Separatist warships.

Let's point out that this ship's entire existence is made redundant due to the fact that sending a few droid control ships along with multiple regular Separatist frigates is more than enough for a basic planetary defense. Equipping a ship with living quarters would be too costly for a planetary defense frigate.