I've played with this a bit (mainly with a red LED) as a single status indicator with multiple states.
It's worth giving it a try with an Arduino, because that gives you PWM very easily and it can drive reasonable LEDs directly off GPIO pins (up to 40mA from one pin). You can put the LED in a box with a lid made of smoke colour (dark grey) polycarbonate or acrylic sheet to get a blacker baseline, but you'll need more brightness than you would for a bare LED. You may be planning on using an Arduino anyway to drive the final matrix.
I found that 50% wasn't dim enough compared to 100% to be noticeably different given variable lighting conditions. 20% was far better. In the end I had one LED with flickering at 10Hz at 20% (ready), steady at 100% (active), steady at 20% (wait).* However in a matrix you might be able to use 50% as you'll have the contrast of 100% pixels to show which are dimmer, and could even go to more levels of grey. If you only want 2 brightness levels you could tune the drive voltage (or easier the series resistance with a fixed drive voltage) to achieve the contrast you want, but then you'd need 2 output pins per LED; with PWM you'd only need 1.
*This was with a big red LED built into a pushbutton, used to fire a single pulse from laser. The piezo-speaker playing pew-pew noises wasn't strictly necessary.