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

First of all, gateways do not have connections. LoRaWAN is not WiFi. Devices connect to the LoRaWAN network server, not a gateway.

To answer your question, current systems redesign the requirement for a downlink after each uplink. LoRaWAN is designed for asymmetric communication, from device to the network, not symmetrical.

Why do you need a downlink after each uplink? What happens if the uplink gets lost (or the downlink is lost or can’t be transmitted due to the gateway running out of airtime)?
Keep in mind a LoRaWAN gateway can’t receive when it is transmitting so too many downlinks will inevitably result in additional lost uplinks. Apart from the usual causes of lost uplinks like collisions, RF issues and the like.