If this is still on the same project I remember...
Then as I recall, your signals are such that, there is little or no sequential logic (i.e., clock signals to worry about tripping with extra edges), and the bandwidth is quite low (i.e. does it light an LED or not), so it's basically not a problem.
Yes, higher voltages do have higher thresholds, assuming you wire them that way. Drawing real current at the same time is also a good plan (e.g., industrial 24V and 4-20mA controls).
When it comes to dumb on-off signals, big voltages aren't ever going away. 120VAC is common in industrial panel level design, since it can be used to directly operate relays/contactors, lights, small motors, etc. 24V (AC or DC) is common for the same reason, with the advantage of being SELV.
As for communications, you're often better off combining signals into a few pairs, usually with something like asynchronous serial over RS-485, or a high level protocol (CANbus, Ethernet, etc.). These are very common in industrial communications, and most PLCs offer built-in support or IO modules with these functions.
Tim