So, general consensus seems to be that the Flood would be more capable at creating ships than basically anyone else and could use the space more efficiently.
As an example, lets say they built a battleship using this small forge world that's about six kilometers in length. On the smaller side of battleships as far as the Imperium is concerned, but it uses that space a lot more efficiently. Lose anything like beds, bathrooms, mess halls, cargo space for stuff like food, basic amenities, probably don't even need human-sized corridors for most of the ship which would help against boarders that aren't squats or ratlings. As a result, you get a very compact warship, probably deadlier than anything of similar length assuming similar weapon capabilities.
When it comes to building the ship, the Flood has the advantages of:
-Perfect/Near-Perfect coordination on a massive scale. Flood forms are able to move as one when under the coordination of a sufficiently large Gravemind or a Keymind. This would be similar to massive automation, but more adaptable to changing situations and less likely to suffer breakdowns.
-Not needing ornamentation. No need to waste time crafting a massive eagle-shaped prow for your battleship or finding and staining glass.
-The Flood is able to dedicate all of its forms' time and effort towards finishing the craft. A combat/pure form isn't going to need to sleep.
-Bending reality via Neural Physics to do stuff faster or more efficiently at a sufficiently high level.
-Optimized building with the mutability and specialization ability of flood forms in mind.
-No bureaucracy to deal with.
-Able to learn and implement better/faster methods on a dime.
Keep in mind that smaller, more compact ships have the downside that a penetrating hit is more likely to hit something important.
There is also logistics to keep in mind.
What type of weapons is it using?
If those are pure energy weapons, they need the energy connection, if it's a weapon that uses physical ammunition, where are the magazines, is it explosive ammunition etc.
While the ship won't truly need to cater to the needs of a crew, it would need to cater to the needs of logistics, as well as the ability to do repairs.
If the ship would be able to fold open like the eldritch flesh origami it probably is, because it doesn't really have internal pathways to access damaged areas or storage areas, then the folds are possible structural weaknesses.
There is also the question of throughput when considering designing the interior.
One advantage the flood has is that it doesn't need communication lines across their ship.
Meaning that the ship can be sectioned off completely.
There could be a compartment completely enclosed by bulkheads and armor that contains the ammo and the weapons, that use ammo.
If it takes a hit that ignites the whole thing, the explosion would go outside for the most part, instead of spreading into the ship.
Anyway, there's usides and downsides to the designs.
I'd expect the flood to use the space that is freed up by not having to use crew and more efficient ways of utilizing things, like simply huge muscles reloading Macrocannons instead of work crews, by adding more redundancies, armor or upscaling existing systems.
Bigger engines, that can run hotter than the orignal engines, same for reactors, shields, weapons etc.
Resulting in something that has the same size, but is more resilient, more difficult to mission kill, faster and more dangerous while also being more salvageable.
The kind of ship that you would think to be dead only to nail you with a broadside when it suddenly rolls around after you had already dismissed it as a threat.