If the history sim will continue will that include soil erosion? For example if your grand project includes damming a river would it experience the problems that a structure of that nature would after say 100 years? if your fortress were built in only soil layers would the traffic and weight of all that hording eventually collapse the tunnels? I guess this would also be a question towards world physics as well. You would have to worry about flooding/earthquakes and retrofit your fortress every couple decades.
I think soil erosion only happens (and will probably continue to only happen) during world gen. It's maybe one of those things, that while even preindustrial societies could have large impacts on their surroundings (the landscape of central Europe was pretty much made by the spread of agriculture; it was all forest before), it's probably not worth the effort to calculate in-game. Floods are probably due to be (re-?)added. But as a counterpoint for whether you have to worry about flooding etc.: the river Tiber in Rome used to regularly flood (with intervals of years or decades), covering huge areas of what has been the city center since ancient times, and they only built high walls at the riverbanks in the late 19th century. E.g. the Pantheon, which is one of the few surviving Roman buildings (if not as well known as the Forums or the Colosseum, but those are mostly ruins), must've been flooded dozens of times, sometimes being under several meters of water.
Besides buildings, and as a counterpoint to tunnels collapsing, catacombs from the Roman Imperial exist at least in Rome and Paris. There were partial collapses probably, but most of the tunnels had remained clear of debris and such, barring what damage grave robbers caused.
So: the realistic way to handle it would for floods to happen, and those areas being inaccessible while it's happening. And leave tons of mud to clean after. Regarding constructions/tunnels getting destroyed, this is something that should probably happen if a fortress fails or is abandoned, maybe even in just a few years, or e.g. progressive damage to all buildings/constructions/partial collapses of at least soil tunnels, once per 10 years, but for a place that continues to be lived in, I think we can assume that the dwarves are doing some abstracted maintenance.