Because he and Ruvkun were awarded for a body of work that began in 1993 and has continued to the present. Lee was only directly involved in that initial - but very consequential - paper. This is the 11th major award Ambros and Ruvkun have shared over the last 20 years.
You're more or less right about the general idea - rightly or wrongly the committee decided that his work was more substantial and extended beyond the part on which she was the lead author - but wrong about all the details. The work began well before 1993, and they worked together for decades.
To clarify further: Lee helped discover microRNA's existence. Ambros and Ruvkun figured out over many years what microRNA *do* The Nobel seems to have been awarded explicitly for discovery *and* function
Not sure that’s a fully accurate version, she was involved in a lot more of the work
Lee was involved in more than that. She appears on 20 papers nearly all of which involve microRNA, c. elegans, and her husband. (Worth noting, though, that he’s been on 138 papers nearly all of which appear to be on this topic.) www.semanticscholar.org/author/Rosal...