I wouldn't say 100 functions over one data structure, but e.g. in python I prefer a few data structures like dictionary and array, with 10-30 top level functions that operate over those.
if your requirements are fixed, it's easy to go nuts and design all kinds of object hierarchies - but if your requirements change a lot, I find it much easier to stay close to the original structure of the data that lives in the many files, and operate on those structures.