While the concept of breaking down blocks to craft others is a more-or-less sound one. Cubatoms were poorly designed from the start, both in usability and power. It is too difficult for the neophyte to grasp the system out of the box without someone explaining it to them in detail, but once they understood it, they basically have access to infinite blocks and credits. But thats fine, its alpha/beta mistakes will happen and many ideas that seem good explode when they hit reality.
Should it be ripped out and forgotten? Ehhhhhh maybe.
It boils down to how you want to craft the player experience. Do you want new players to have to build infrastructure and climb tech-trees, or do you want them to land on any planet or asteroid and within a short period of time have the same construction capability as someone who has been playing for a week?
It isn\'t an easy choice, both have their problems.
The first obviously requires a heavy player time and knowlege investment, which, if we are going to use something like Gregtech Hardmode as an example, has a lower player retention rate than regular Gregtech, and even less than plain Ic2. But on the other side, if you have ever gone from 0 to fusion reactor, in HM, you will feel a pretty good sense of accomplishment.
As for the second, which is mostly what we have now, it leads to a somewhat shallow crafting experience; but this puts the emphasis on the construction of ships, which, is certainly the primary selling point of the game at the moment.
Cubatoms, or a system which works very similarly to them, work better with the latter. It may cater more to the artisinal ship builder over the industrial one, (but that is a different and somewhat unrelated problem.) However, they work very poorly with the former. The more in-depth you want your crafting and infrastructure system, the more difficulty you will have balancing it. The power to craft anything from anything is very powerful, to the extent of negating every other resource once it has been reached. To reference Ic2 again, it was for this very reason that UU matter has been nerfed again and again since its introduction to the point of near uselessness (even then its better in some cases to mining).
So in the end, If you are going to add things like shipyards, drydocks, more in-depth crafting and industry system, cubatoms or a system like them will be poison and you will be struggling to keep them from breaking down the system or being relevant to it.. But, if you aren\'t going to change things much from how they work now and leave resourcing your ships a relativley simple thing, Cubatoms are pretty much fine the way they are with a bit of reworking to get rid of infinite loops and make it less arbitrary and more user-friendly.