You can find the schematic of the Uno here: https://store.arduino.cc/products/arduino-uno-rev3.
Look for the ICSP header and see how it is wired.
How many times did you look at the Adafruit SD module with level shifting ? https://learn.adafruit.com/assets/35635.
So yes, the unused inputs are connected to GND.
I don't understand what you have done with the leds.