Yes. Devices can be connected with USB in several modes. Only if USB debugging is working correctly then you will be able to connect the IDE (or Eclipse) to the device, not using B4A-Bridge. Basic4android uses ADB (a tool from Android SDK) to communicate with the device. So the problem is usually not in Basic4android.
Maybe in the future. You can choose compile & run and ignore the last message. In most cases developers are able to connect to a real device using one of the three methods: USB debugging, B4A-Bridge over wifi network or B4A-Bridge over bluetooth.