As far as I know, there is no way to talk from Node-RED to HomeKit enabled devices using the HomeKit protocol. Apple only publish the specs for client devices and services, but the HomeKit server, and therefore UI, can only be iOS device. You can think of HomeKit as the Apple alternative to Node-RED. And the control can only be one way - from Homekit to Node-RED. You can make the data flow both ways though. For instance you can create virtual HomeKit switch in Node-RED, that the Home app can control using automation (like turning on when you're home). Thus you can have binary communication between them.
The protocol actually specifies a set of predefined accessories with their options and capabilities, and each manufacturer should provide API for the selected accessory. One physical device can have multiple virtual accessories - like temp and humidity sensors, that are shown as two items in Home app, but might be one actual device.
You need to use your iPhone/iPad to add and control the bridge/accessories, that you can create in Node-RED or are licensed HomeKit devices. But they are not able to talk to each other using that protocol. You'd have to find alternative way for doing this by looking for another API by the manufacturer. For instance Hue is certified as HomeKit and you can add it to your Home app directly, but if you want to control it with Node-RED you'd need their other API as the HomeKit server is proprietary.
Also for Node-RED use the updated
node-red-contrib-homekit-bridged that can simplify your management.