Synthesis of Nios II Processor

Quartus II will analyze (parse) any file in the project files list. But it only elaborates something if it's part of the actual design hierarchy. I wouldn't study too critically the elaboration or synthesis of IP.

The attribute warning you reference comes about because parts of the NIOS II code were originally developed using a third-party synthesis tool that supported such an attribute. However, QIS doesn't support the attribute, which should probably just be removed from the design files by whoever develops the NIOS II code. For now, you can simply ignore the warning.