After they sleep together in the past, wouldn't she recognize that this is the exact same person when he grows up?
No, she wouldn't. Children and grand-children typically looks a lot like their parents and grand-parents.
She'd have been much older and have a worse memory. Also, to my knowledge, it never specifies if she's even alive at that time. Fact is, you wouldn't remember something like that after many many years.
Two reasons: She may have already died by 1999 or she may have just though to herself 'he looks a lot like his grandfather'. It never would have occurred to her that he had traveled in time.