"I too-indiscriminately set dwarves to deconstruct constructions, and then later noticed open space where I thought no open space should be. The stockpile continued to exist, which masked the open space, but the space is perfectly visible from 1 z-level above. Any items formerly in the opened space were moved to the location of the deconstructer as well as the floor's construction material, but that's not unexpected.

I'm using PeridexisErrant's latest LNP, including DFHack, though I think the only way that affects anything is fixing the vacuum cleaner effect that pulls in everything in a 16x16 block near the deconstructor."