Systematic data pauses between gateway and application

Up to date versions of LMIC do include this. As do older versions. But you have highlighted why ABP sucks.

This is most likely hardware related as I have nodes on hundreds of thousands of uplinks on LMIC on ABP

By freezing do you mean the debug serial log isn’t showing any more info? [Please think ahead to what information will help the volunteers with answering] Do you mean downlinks which is the end device receiving? If the firmware has frozen then nothing a gateway transmits is going to cause a device to restart.

As above, I’ve devices that are doing just fine. But getting LMIC in to an ATmega328 leaving room for local variables takes some configuration. What optimisations have you implemented?