They can only be healed by their commander ships, which have an ability that uses promethion to heal all ships in a fleet. This lack of healing isn't as bad as it seems since all their ships have twice the hit points compared to ships of other races. This means they can survive longer than other ships.
The Onyx Hive are silicon based, so their growth rate depends on the amount of promethion they have. This means a decision has to made on whether to use the promethion to repair ships or keep growth rate high enough to get more Onyx Hive in a reasonable amount of time. I find them interesting to play. They require different planning and choices.
Things to consider for custom races are:
1. Use promethion born ability or not.
2. Use silicon-based race or not.
3. Use Onyx Hive ship set or not. This determines if commander ships can heal other ships or not. Only Onyx HIve commander ships in the Onyx Hive ship set have the ability to heal ships in my mod.
I haven't tested all of these, but the wrong combination can cripple a custom race. The promethion ability without the Onyx Hive ship set means there is no way to heal ships with my mod. Without my mod, some items are available in the shipyard to put on a ship. I'm not sure if the game will automatically design ships with those items so the player and AI can have ships that heal or heal other ships without making a special design. I'm also not sure if the healing actually works.
I don't know what the original intention of the develops was when it comes to how the promethion born ability, the silicon-based biology and others things were supposed to work together. Maybe I'm wrong to remove some things in my mod. Without my mod, some ships might be able to heal themselves or other ships, which I think goes against what the ships aren't supposed to be able to do.
As a final note, there is an artifact called Mnemonic Nanites that sometimes can be found on a planet. It can be used to fully repair a ship or fleet. It works on promethion born ships, which I think is acceptable. The artifact is rare and special, so I think its ability to repair promethion born ships should stay for an occasional bonus.