How long does mongodump take on that database? My experience was that incremental filesystem/blockdevice snapshots were the only realistic way of backing up (non sharded) mongodb. In our case EBS snapshots, but I think you can achieve the same using LVM or filesystems like XFS and ZFS.
It takes ~21hrs to dump the entire db (~500gb), but I'm limited by my internet speed (100mbps, seeing 50-100mbps during dump). Interestingly, the throughput is faster than doing a db dump from atlas which used to max around 30mbps
