I'm still battling the idea that all the races bombard the planets inhabitants and why they don't foresee this and start to dig into bunkers far underground to survive.
Consider that the bombardment infrastructure upgrade... doesn't change the fact that with enough power,
any bunker can be breached.
Perhaps time plays accelerated but that still leaves one question about how the ships crews would appear to live forever...
How do crews "appear to live forever"? You can always use smaller craft, conceptualized into the background, to rotate your crews, just consider that as not being incorporated into the gameplay, so you don't have to worry about that kind of micro.
Also, if all the factions have the power to so easily nuke a planet they don't really have the use for money. They build Crystal and Ore mines and build ships from that. What good is money when you have this awesome power already. Considering you completely annihilate a population you're already a dictator of the worst calibre.
I'm sorry, but thats a complete non sequitur. Money makes the world go round whatever century your in, or however much power you have.
To add some variation for future updates and additions to the game, why not a race with bio-engineered ships who instead of bombarding planets gather the biomass from the planets to construct their ships and stations. Crystals and Ore would have less use for them, perhaps only to create an exo-skeleton structure which in the end would feed off planets to create their bio-engineered ship station, having to be careful not to drain the planet too much while doing so.
"Easy to learn, hard to master".
Thats the concept behind much of the game. Your idea of a "bio-mass" based race would complete violate the core game design... and not really add anything.