Some shells, such as elvish [0], nushell [1], mash [2], and even Windows' powershell do support natively manipulating structured data. There is quite a gap between the shell supporting it and tools supporting it, though, and it's a bit of a chicken-and-egg problem.
[0] https://elv.sh/
[1] https://www.nushell.sh/
[2] http://mash-shell.org/