The US cryptography key is only needed for NATO Link 16 communications, not for regular flight operations. This is totally normal because Austria isn't a full NATO member. They are part of the NATO Partnership for Peace program which allows for limited levels of cooperation.
But right now the fact that there US citizens (apparently civil contractors, not military personell) stationed at austrian air bases to enable some functionality is a big deal. This is a big deal because the wish-wash Austrian Neutrality is crucial to Austrian Identity.
How is it a big deal? If Austria wanted full access to NATO technology then they should have joined NATO. They chose not to, and now they have to accept the consequences of that choice. Can't have your cake and eat it, too.
It's the usual hypocrisy. There never was money for the military, neutrality ever popular and nobody thought about it back when things seemed more stable. Now that things are changing, it's a big deal. Maybe we join Nato, maybe Europe get it's own shit together. We'll see.