The underground doesn't need to be made infinite. I personally think making it infinite would be a terrible idea, not just because of mod added quarries and such. For starters, vertical movement is a pain. Digging really deep means it would take forever to climb back to the surface. It would also be much easier to get lost. Plus, people in modded servers would need to restrain themselves more when using chunkloaders, since having infinite chunks up and down would mean you would be able to cram much more lag inducing things into closer proximity of each other.
A deeper world limit would still be cool though. I personally think the Minecraft underground should be deeper, and even more high-risk high-reward the deeper you go. That said, even if this was implemented I still think the underground should be cut off by bedrock at some point like it is now.
Lol chunk loaders have infinite up&down because that's the way minecraft chunks work.
I imagine if cubic chunks were implemented you'd choose a 3 dimensional area like a cube or a sphere in the chunkloader.
Otherwise I agree that infinite down is not a good idea.
As for the actual idea of cubic chunks, I very much doubt mojang hasn't thought about it because when I first learned about chunks I thought 2d chunks were weird .
My guess is they thought at the time that they wouldn't get major performance boost out of it and it'd be too much of a hassle.
But if they keep going for big mountainy landscapes it might be a good idea.