Is there any way that arbitrary code in the file could compromise the user's system? If so, does the user know to treat these data files as executables? Is there any way someone untrusted could ever edit the file without the user's knowledge? Even in combination with other programs the user might be running? Are you sure about all of that?
Maybe Lua in particular is sandboxed so that's not a problem (beats me), but in general this is an area where safe high-level languages can all of a sudden turn dangerous. Personally I would rarely find it worth it.