I would say APL-family languages today have largely addressed these concerns with operators such as Key[0][1] and nested arrays. J also has built-in support for sparse arrays. Some more complicated things like storing a list of lists in a compact representation (perhaps lengths and data) aren't supported natively, but I'd consider that a niche concern as a list of lists will have similar performance, just with more memory use.

There's a lot of database software built on array languages, with kdb and Jd being the most prominent as far as I know.

[0] https://aplwiki.com/wiki/Key

[1] https://code.jsoftware.com/wiki/Vocabulary/slashdot#dyadic