gp2 EBS as far as I recall get IOPS allocated based on size. I think it is 3 IOPS per GB so I believe your disks would only support 300 IOPS, which is not a lot. This could very well be the limiting factor once indices grow and larger, I/O intensive merges take place. You may want rto test upgrading or increasing the size of your storage to see if that makes a difference.