Version of InDesign? Operating system?
Exactly what command did you use to create the Hyperlink? What kind of hyperlink (URL, page, email address, etc.)?
Exactly what command did you use to export the SWF file? What browser are you using to view the SWF?
Did you try previewing in the SWF Preview panel?
using Indesign CC(2014) & win7.
we use the hyperlink for URL.
we use the google chrome to view the SWF.
We try previewing in the SWF Preview panel, it is work.
but export to the SWF and the google chrome is showed up, it doesn't work.
even we had re-installed Indesign & Adobe flash player.
It could be a limitation in the Chrome browser. Try another browser.