Are you concerned about ‘it not working’ as a result of the missing port?
MIDI ports are ‘dumb’, and LED’s are even dumber.
They are just points where electricity is transformed into something for human’s to interact with. A Light in the case of the LED and an electrical digital signal in the case of MIDI.
In both cases the signal they get come from some circuitry that connects to the Input/Output pins on the PI.
This circuitry ( the encoder board, if you’ve used one) takes the tiny amount of energy from the raspberry Pi and amplifies( buffers) it to the sorts of levels that would turn a LED on ( 3.3V * 12mA = 0.04W) or generate the MIDI signal as a switched current in the circuit to the MIDI port at the MIDI input of the device you are connecting to.
There are Three different MIDI ports.
MIDI IN: An optically coupled ( to prevent ground loops and protect you from electric shocks on equipment connected to the MIDI IN Port)
MIDI OUT: A current source designed to put enough current down the MIDI loop to turn on the LED in the opto isolator on the MIDI IN connector it’s connected to.
MIDI THRU: A ‘copy’ (buffered) of the MIDI data coming into the MIDI IN Port that you can take onto another MIDI device to allow a Master keyboard (for instance) to control upto 16 different instruments.
You don’t need MIDI Thru, and the Zynthian it’self knows absolutely nothing about it. It’s a pure electrical copy of the Input and is in no way controllable from the zynthian’s point of view, but it’s really handy to have it if you are using 5 PIN MIDI connections.
Similarly all you do by leaving of LED’s is reduced the current consumption of the overall device ( And live in a slightly darker environment…)
In old fashion Analogue synth buildings days you could often hear pitch changes in the oscillators of synths which was down to a the LED’s all flashing at the same time and the Power supply changing it’s voltage slightly. . . . Which is why some people build modern synth’s the Zynthian way . . . .
Hope it helps.