The Description on the download page says that Aquasnap works with multiple monitors.
https://portableapps.com/apps/utilities/aquasnap_portable
However, The Home page of AquaSnap now has a button that allows you to buy a license. The page that it brings you to indicates that multi-monitor support is a feature that is disabled unless you have paid for a License.
http://www.nurgo-software.com/products/aquasnap/28
In short, from what I can tell the the paid version has multi-monitor support while the freeware version does not.
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