make them mining planets instead.
Unless it's economically viable to move the industry that makes use of the resources you could get out of an uninhabitable planet to the uninhabitable planet or unless it becomes incredibly inexpensive to lift useful quantities of resources out of a large gravity well and ship them to the point of use, it's rather unlikely that mining an uninhabitable planet will be economically viable as long as there's anywhere else you could go to find that resource that isn't a larger uninhabitable planet or a star or something like that. Just about any resource you could name should be available on an inhabitable planet (possible exceptions are mostly only things that require living things to form, such as petroleum and coal, but these kinds of things are less likely to be available on uninhabitable planets than on inhabitable planets) and most of these (again excluding things that require living things to form) can be found in asteroids, which are a far more practical extraterrestrial source of resources than an entirely separate planet.
What is the difference between a "class 0" planet... and a Barren planet? Mercury is depicted as a rocky class 0 so is Venus in the game
A class zero planet is a planet which lacks economically-exploitable land in sufficient quantity to support a large enough population and industrial base to matter at the scale of the game. A barren planet is a planet which lacks any significant biomass prior to the time of colonization (at least in the near past), and so most or all of the requisite material to create a sustainable biosphere on the planet will need to be brought to the planet, likely making the colonization project more expensive and more difficult than would be the case were an existing more or less compatible biosphere already present upon the planet's surface (and it would appear that GCIII assumes that any biosphere present on the surface of an inhabitable planet is more or less compatible with all current species found within the game, barring one of the 'extreme planet' conditions). "Barren" and "class zero" can overlap; Mercury and Venus both lack any significant biomass, and Venus in particular is exceedingly unlikely to be economically exploitable for any purpose (its very high atmospheric pressure at the surface and its very high surface temperature should make it quite expensive to attempt to exploit any resources or create inhabitable regions on the surface, and its very thick and dense atmosphere combined with a surface gravity similar to Earth's should make it quite expensive to get anything off the planet even if you can economically do something on the planet's surface); Mercury's highly-variable surface temperature is also problematic for permanent structures.
In make believe what would keep us from colonizing any planet. aka Jupiter arising. If they can colonize Jupiter why can't I in the future. Just remember one thing the Ai should also do this.
As long as there are inhabitable Earth-like planets available, why would you bother "colonizing" Jupiter-like planets? It's generally more economical to colonize a location which is already more or less capable of supporting life than it is to build an artificial structure which is sufficiently large to host a population of a size that matters to the game with sufficient agricultural output to support said population and a large enough industrial base for said population to be able to make a meaningful contribution on the scale at which the game operates. For that matter, if you're capable of building inhabitable artificial structures of this nature, why only build them around gas giants like Jupiter? Jupiter and its moons are nothing special as far as economically-viable resource deposits go; most of what you could source from one of its moons could likely be extracted more economically from an asteroid, and it's not like Jupiter is going to be an economical source for any kind of resource except maybe some gasses extracted from very high up in the planet's atmosphere.
On top of that, it's not at all clear that building a sufficiently large artificial structure to support a large enough population and industrial base is within the capabilities of playable GCIII species. Even Economic Starbases appear to function more by streamlining existing processes than by creating output, and it's certainly the case that even the Economic, Mining, and Cultural Starbases do not host populations of sufficient size to be taxed to a degree which offsets the upkeep of the station by any appreciable amount.