True. Don't be apprehensive about depth/complexity. A comment line or two may be sufficient to document the structure if you need to go back and tweak it. Here's a one line comment from something I wrote several months ago.

polls->{lane:stage}->[row]->[col]

This is sufficient to remind me how the data is organized. Polls are polling cycles over time for chip insertion machines which may have one or two lanes/stages. The row/col are defined by a header row of words for the column labels. Values corresponding to those header row words are in subsequent rows.

This also illustrates one thing I frequently do. I often use and store my hashes and arrays as refs. This makes it easy to pass everything as a scaler. For example, I have one package to handle the processing of one part of the data. If I need to store that, I just get and store the ref to combine the individual pieces to a higher level. This type of organization allows the use of OO concepts others have mentioned, but does not break/remove the built-in features for using arrays or hashes. If all of your data is in one file, this may not be needed. But, it is a handy pattern that can be used in other situations.