I'm having the same issue on Linux, and am already using version 45.0.2552.812.
I have tried with the hardware acceleration on and off, and have also tried with both Pushbullet and GMail, but none of these display desktop notifications from Opera.
Desktop notifications are working from both Firefox and Chromium under my current setup, so I know that they should be supported.
I am happy to carry out any additional testing required to help diagnose the issue.