How a gateway deals with 100's of nodes and keep withing message limits

TL; DR: You’ve picked the wrong technology.

As we have no idea what the uplinks are from or why there has to be a corresponding downlink, there is no way to advise if there is an implementation that would work.

As noted above, given the shared use of the ISM band, you may have even picked the wrong communications system all together because:

They don’t because there is no need for the designed use cases for LoRaWAN. Or indeed any user that is using license free radio spectrum as your gateway, LoRaWAN or any other system, will likely breach the legal transmission duty cycle.