Let me quote what’s mentioned in the official FAQ of WordPress.com Stats plugin (JetPack statistics module uses this plugin as the base)…
The plugin collects stats via a javascript call, so as long as the JS call is on the page stats will be collected just fine, whether the page is cached or not.
In short, you don’t have to worry about JetPack stats. It works irrespective of the caching layer/s used.
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