Terrorists abuse the rights many law-abiding worshippers have by using Mosques to conceal the planning and orchestration of horrific acts. Obtaining surveillance warrants is a long and complex process of law enforcement agencies. Many people view police observation of Mosques as illegal profiling and discrimination. The terrorists use this to their advantage.
Terrorists must be tracked down wherever they go. It is a matter of national security for Germany (and many other countries). A "raid" on a mosque can be done respectfully, following proper procedures, such as obtaining warrants and following other safeguards. But a mosque cannot serve as a haven for terrorists.
Terrorists are using mosques to hide from law enforcement. This is because the government has not fully found a way to infiltrate the Muslim religious sect. There are language barriers, barriers in dress and physical appearance, and lack of familiarity with their culture, which prohibits some easier access to American Muslims.
Yes, terrorists may very well be using Mosques to hide from law enforcement. This should not be surprising. Criminals have been using houses of worship as hiding places for a long time. One would not expect a Muslim extremist or terrorist to use a Christian church to hide. That would be counter-intuitive.