Does Datadog support graphs with 2 Y-axis with different scales?

They do allow dual y-axis now

https://docs.datadoghq.com/dashboards/widgets/timeseries/#y-axis-controls

Introducing dual Y-axis for time series widgets. The time series widget on dashboards now support dual y-axis, making it easier than ever to compare two sets of data on a single graph. By removing the need to create separate graphs, your dashboards can show even more valuable information viewable at a glance.

2016 Confirmed on IRC (#datadog on freenode) that:

Datadog doesn't support multiple Y-axis at this time.

2020: Now it is supported. See James' answer below.