I use Neovim instead of Vim9 so I'm not entirely sure, but going by the format of the rest of your config, wouldn't it just be something like

var pylsp_config= {'pylsp': {'plugins': {'pylsp_mypy': {'enabled': true},... }, }, }

?

Maybe this wasn't there when you originally asked the quesiton, but thepylsp-mypy README shows all config options prefixed withpylsp.plugins.pylsp_mypy., the first two parts matching the "upper layers" of your existing config example. Hence why it seems correct to me.