The multidimensional hashes were actually used for multidimensional array (or hash) emulation, before references were added in perl5 to make those and more complex structures far easier. The old style is still supported, but modern reference-based structures are almost always preferable: see $SUBSCRIPT_SEPARATOR.

Also, there is nothing wrong with multidimensional arrays. In fact they are so useful, they even have their own manpage: perllol.