End-to-end encryption only protects messages from being read while "in transit" through cell providers, the internet, and Google/Apple's message sniffers. It does not protect them from viewing them directly on the phone. When the search warrant was executed, they took the cell phones and had Google/Apple remotely unlock them. This type of request requires a search warrant which they did have.
Signal application is not as safe as you think it is. Yes, it has a passcode to enter the app. Unlike fingerprints, and phone passcode, which can be bypassed remotely, the Signal passcode is specific to the app. Google/Apple cannot unlock it. That said, Signal only requires you to enter the passcode after several days of application inactivity. In other words, if you use the app daily, you will never need to re-enter the code.
Anyone who thinks they have secure phones/apps are grossly misinformed. There is nothing you do on your phone is private or secure. Nothing.