Certainly if they were to build anything it would be to repair machines or rebuild destroyed machines from scratch, though allowing them to do so presents a ton of other complications, such that it hasn't really been deemed worth the amount of work it would require to implement it. It'd be nice to further improve the atmosphere and immersion, but there are other more valuable features to work on first, before that could ever happen.
In terms of building
new stuff, the only place really "missing" props would be the lowest depth, which is obviously in the early stages of being expanded as you awake. But it's not an area to hang around anyway, so adding stuff there comes off as a pure fluff feature. (Note: I also actually made a little change down there for the next release).
I could have them put the occasional machine in an otherwise empty room, though the numbers of those machines are already more or less balanced, so this would be a "remove a machine and let them install it later" kinda thing. That'd be neat (I've done it in other situations some players will have discovered), though again it wasn't built into the system to begin with so it'd take a while to get something like that up and running. In any case, this has actually been among my plans, but it is very low priority so I don't know if it would come to be. (If I were to work on Cogmind indefinitely then, yes, it's inevitable, but I'm going to have to stop one day!
)