One possibility is that since the app didn't work well on Windows Phone 8.1, WhatsApp decided to take it down until its tech team could offer a version that works with Windows Phone 8.1. This way, no Windows Phone user will have a bad experience with it, while waiting for a version that will work with the updated platform.
WhatsApp is waiting for foreign regulators to give the all-clear sign to Facebook's $19 billion acquisition of the company. Last month, the FCC approved the deal on the condition that WhatsApp and Facebook follow through on the promises made to WhatsApp users before, during and after the bid was made by Facebook. The agency wants to hold Facebook founder Mark Zuckerberg to his promise that "We are absolutely not going to change plans around WhatsApp and the way it uses user data."
As far as Windows Phone users are concerned, it all doesn't mean a thing unless WhatsApp returns to the platform.
source: WhatsApp via WPCentral