Without having any proof, I assume the data structures populated from raws are all created/read during world gen, with potential additional entries added as part of the world gen (e.g. syndromes). I see no point in ever removing any entries as they're not that many, and in many cases they don't even have numeric identifiers (e.g. creatures and plants), with indices being used in other data structures. If any changes would occur, they'd probably be in the form of new entries added at the end. Even if you were to make modifications, such as e.g. a ritual that turned all strawberries blue and poisonous, you'd probably still have to keep track of the old kind (e.g. in a depiction of a dorf eating a strawberry), from the new kind, hunting down and replacing all applicable entries (i.e. all the berries and plants in existence).
Similarly, I'd suspect art and art forms only grow through addition at the end of the vectors, with nothing being removed.
Regardless, if you access data while DF is running, you'd have to determine whether it's probably safe on a case-by-case basis.
Also note that nothing is safe from DFHackery, but I'd rather use a disclaimer for that case.