Parts of the government aren't that great at secrets, sure. But like someone else wrote, the government isn't a single entity, but a collection of entities. Moreover, a substantial (if not the vast majority) of classified work is performed by contractors (SRI, Lockheed etc) which have their own procedures in place.

We know through OSINT that the government has kept plenty of secrets and they have done so very very well for decades, before leakage or disclosure. Finally, with such a poor SnR these days due to information overload and psyops, even if the government isn't that great at secrets, you still have the herculean task of sorting through the information haystack looking for the needles.