From the article "but they [the companies] can be forced to keep quiet about it in order to avoid exposing active investigations and alert those targeted by the probes."

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)