But given the number of things that can be voted on in Switzerland if you get enough signatures, is it that hard for it to be blocked?
At federal level you cannot vote against financial decisions taken by government organizations. The Gripen buy could be voted down because a law was drafted to create said fonds to finance it, and to allot that fonds to the military as a rise over its default budget. That law was opposed.
And how could the military fund such an acquisition within a budget which is so tight it's not funding out of office hours air policing?
The Swiss defense budget isn't tight. They spend as much on their military per citizen as most EU countries (about 1% more than Germany, for reference), and their budget is currently on a continuous rise until 2017, with +30% defense expenditure over 2007.
In fact, in both 2012 and 2013, the defense department had considerably
more money available (by allotment from the government) than they ended up spending - the money went back to the government to build additional financial reserves with. That's where the +0.7% that would be necessary for 24/7 air policing could easily be paid from.
The Gripen buy as planned would be ten times that btw. The budget is rising by just that amount over the next two years. Entirely outside of the money that was planned for Gripen, which was the same amount again.