Looks like you already thought of the false reflections if the receiver module's emitter is blasting away - albeit at an angle that should never come back. I've read about the empty flat-car issue if you place the beam too high but I'd think all that can be adjusted to your cars.
Yes, it's clearly expedient to just half of each module. No need to cover the unused receiver. Frankly, ideally you would not just cover the unused emitter but cut it off the board! The problem is it consumes a heck of a lot of current...some 10 times more than the receiver half of each module! But no worries.
I'm curious about how you're going to mount/hide/disguise these. You can of course carefully bend the leads of the emitter and receiver if they are long enough. Separately there are modules on eBay that only have the emitter and receiver components themselves. Just apply 5V and the emitter operates; the bulk of the circuitry on the modules is for the receiver and its sensitivity adjustment circuit. This "bare" module may help with space issues on the emitter side...assuming you don't want to de-solder the emitter from one module and run it under the tracks...
