There are a number of reasons why both the government and the companies would want to keep it secret:
1. Bad reputation for the company.
2. Bad reputation for the government on how much spying they actually are doing.
3. "keep quiet about it in order to avoid exposing active investigations" (this point I would think to be irrelevant in this case however)
I think they should be punished by law to the fullest extent available. Along with everybody that was responsible and is within the reach of EU law.
Actually, the EU should request extradition of those responsible that reside in the US, even if they didn't break the US law. Fair, isn't it?
Which are much the same reasons why someone who has stolen a TV would want to keep that secret. It doesn't make it an idea worth encouraging.
I reject the idea that a US law is more important in Europe than an European one. If that is what has happened, then it is wrong.
If nothing was hidden, why is this policy only coming to light after the fact? There seems to be some degree of not wanting people to know.