Mrs Woodhouse, (or her match makers - arranged marriages were not unheard of then) might have been using her head rather than her heart when it came to selecting a husband.

Mr Woodhouse was wealthy, he did not have scads of children from a former marriage, he was of excellent family, easy temper and could provide a good home.
Uncertain health and certain wealth, can make an older man very attractive to a woman who is looking to her future and would like independence.
Without supposing too much about her feelings or her situation as a single woman, if the only thing against the match is that she is a lot smarter than her husband, and she was as quick witted as Emma, she would be waiting a long time to find a husband that could be her equal in all respects.