May I ask what is this dark spots on my macbook apple logo?

That would be totally up to you. If you purchased this notebook, within the last 14 days, you have the option to return it for a full refund or get a replacement. Otherwise, it will be up to the Apple Technician to determine if it is a manufacturing defect and provide you with your options.

Only guessing at this point, but since they appear to be symmetrical, it could be that they are minute manufacturing imperfections ... possibly caused by air bubbles?

Cosmetic imperfections. How does the Mac run?