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It could be a different hardware model or more VMs sharing the same disk.

Or is it possible that in different data centers different hardware is used? I thought it's supposed to be the same.

The thing is that higher latency affects the whole system hosted on the droplet (Mongo database).

So it's possible that other websites hosted on the same VM affect latency of my droplet's SSD?

Ask yourself the opposite: Could there perhaps be a measurable difference if I am the only VM on the host, versus a ton of busy VMs next to mine?