I would think that the way Hype deals with protocols would be just to pass on the url to the browser and let it deal with the protocol. I say this because I have used
'applescript://com.apple.scripteditor/?action=append&script=...' In the open URL field before with no problem.
I could be wrong but it would make more sense to let the browser's engine deal with these rather than code everyone of them..
Put this in the URL field and see if wrapping it like this helps.
Protocols like this are like helpers. When you use them the browser looks for a corresponding Application that is registered to deal with the url.
As in my applescript example above:
If you are on a mac then putting this
in a link will open Applescript and offer you a new Applescript.