Hi Joan.
Why aren't they living on the surface? Would it matter if there were seas and oceans above ground?
This is stream of thought posting, so please forgive me if I ramble (which I often do).
A number of problems I can think of.
You're right - if the water had time down to eat through the limestone, it would probably have time to eat out through the limestone as well.
If you have plate tectonics, it will split the land and release water into a depression, causing a sea, and once that happens, it's difficult to put back in the box.
The water flows into where? How do you complete the water cycle?
So, problems are there to be solved.
Could you have only some of the land with cave systems? That might prevent the ground from simply caving in. Hard stone with something like limestone seams for the channels to eat away. There are others who know their geology much better than I do. Too many chambers close together would make the system unstable as well, I imagine.
You'll need a few seas, and possibly some massive lakes with collapsed ground above (similar to some of those in Central America (I think that's where they are), but bigger). That would allow evaporation for the water cycle. I know that means bigger seas, or more of them.
Hope some of that helps.