Reaper should send the Corresponding signal to the Streamdeck when you press the Mute buttons.
In the Mackie protocol, a button and its associated LED (=button state) are two completely different things. When you press a button, it will send 127, and when you release it, it will send 0. If the button has an LED, the daw might respond with a command setting the state for the LED. Neither a real Mackie device nor the plugin has any local link between button press and state; it is completely controlled by the daw. Hence, if the button state doesn't change, the problem is in the daw, not the plugin.
In short the Midi plugin is doing fine. It's just that Reaper doesn't send the Corresponding data back to the Streamdeck that is why it is not affecting the state of the icons.
We're hoping this Reaper issue will be fixed soon.