There's nothing wrong with your use of a HoA. It is true, however, that a lot of thought should go into selecting the construction of complex datastructures. The right layout makes all the difference in code complexity/simplicity.

This is even more true when you try creating an artificial neural network in pure perl...  :)  Except in NN's it is normally three, or more, levels deep (AoHoH, HoHoH, etc.) and the code to transverse such structures can get a little intresting.