I could completely remove the Nano and connect the light barriers directly to the Mega analog pins, but then I have a problem of them floating when no light barriers are connected.
Internal pull up can also be enabled on analogue pins.Better tell us the who/where/what/when/why.Joining two processors is not always a good solution.
powered from a separate 3.3V buck...
can I power the Nano from the same 9V and connect 2 digital output pins to 2 digital input pins on the Mega? Or would it be safer to use another buck to get 9V for the Nano?
What kind of signal do the light barriers send to the Nano? Is it an analog voltage varying between 0 and 5 volts or a digital level that is either 0 or 5 volts?
Why?A Mega has a dedicated 3.3volt regulator that isn't used for anything else on the Mega, and it can provide up to 150mA.You might not need a separate supply (you should know the current draw of that display).Two supplies could result in phantom-powering through the I/O lines, which is bad.
Just connect the 5volt pins (and ground) together, so the Mega powers the Nano. The Nano itself only draws 30mA.Don't know what the LEDs in the light barriers use, because you didn't post a circuit diagram.Merging the code and removing the Nano would be easier though.