“I’m afraid” is often used to introduce bad news or something unfortunate. “Not so good” means “not feeling well” or “not doing well.” So the full meaning is: “Unfortunately, I’m not feeling very well.” A more natural way to say this would be: “I’m afraid I’m not feeling very well.” or “I’m not feeling so good.”

It's like saying, "unfortunately not so good ."

Yes, "I'm afraid not so good" is a polite way of saying "I'm sorry, but I'm not feeling well." The phrase "I'm afraid" softens the statement and makes it sound more polite or cautious.

Keep the context in mind to have a better speculation… the expression “I have a nausea” is a good clue here..