I'm setting the safariAllowPopups to true in the device desired capabilities. But for some reason it seems that Appium is not passing that setting to the device (window.open is not working, and when checking the settings page, Safari is still set with the popup blocker on)
I'm using Appium 1.3.6 and testing on iPhone 5 with iOS 7.1 and 8.1
Looks like this might be fixed in the upcoming 1.4 release: https://github.com/appium/appium/pull/4928.