Note 1: (Half a dozen natural children)
As with the earlier introduction of Harriet Smith, the term natural child connotes illegitimacy. Emma's fear here is that Mr. Churchill had children with someone other than his wife. If such flesh-and-blood children existed, Mr. Churchill might wish them to inherit Enscombe, instead of his more distant relative, Frank.
Note 2: (wonderful)
Here the word wonderful has a more literal meaning: that which inspires wonder, as opposed to the more common: greatly pleasing. Frank's announcement has filled the Westons with wonder that he should have been engaged in such a way, and that he should have endeavored to keep his engagement a secret.