Let me turn this around at you: Why would you think that an organism could survive in space when science has never discovered anything like that?
Let me introduce you to
Mr Tardigrade. He and his people can survive absolute zero, vacuum, intense radiation and so forth. And he and his ilk are just dumb creatures that evolved into indestructibility. If you had the ability to manipulate genes, you could certainly create things that can survive in space. other than that, your argument seems a little off. science hasn't discovered anything to implicate that crystals can be sentient either and yet we accept Chenjesu at face value.
All in all, I'm not arguing that living organisms are inherently superior to mechanical solutions. But I don't think they are inferior either. Cells are pretty much miniature factories, capable of creating any and all necessary building blocks for pretty much anything. An organism that is resistant to vacuum doesn't need a hermetically sealed ship,although they would need isolation to keep the warmth inside. Self correction of the genome can protect against radiation (although not that well in the Mycons case). How the weapon works I have no clue, but organic materials can store energy pretty well here in Earth. Perhaps the whatchamacall it secretes an enzyme that triggers a meltdown reaction in their bodies. Screaming in soundless agony they float through space, giving their very bodies for the welfare of Juffo-Wup.
Beyond anything else, the SC races show signs of specialisation. I don't think it's a great leap of faith to assume that the M:bots are pretty mechanically advanced while the Chenjesu use a lot of crystal technology and the Mycon use biologics. Ifti makes you happier, I guess one could argue that the Mycon ship is an example of why biological ships aren't in great demand, it's big, slow and clumsy.