Using Espruino to build a Nintendo Joy-Con like controller?

I am still reading on the HID documentation. I wonder if it can do two way communication

It is! You can get a NRF.on('HID',... event back - it's usually used for caps lock/etc lights but you can send other stuff that way too: http://www.espruino.com/Reference#l_NRF_HID

Had you tried just pairing a normal Bluetooth HID device (even if that was an Espruino) with the Switch? It may 'just work' without having to fully emulate the Joycon?

But I'd have thought it wouldn't be too painful to implement the Joycon's Bluetooth HID profile (which I guess you could dump if you paired it with a Linux PC?)