According to Wikipedia, he only married twice:
https://en.wikipedia.org/wiki/John_Napier
Family
In 1572, Napier married 16-year-old Elizabeth, daughter of James Stirling, the 4th Laird of Keir and of Cadder.[33] They had two children. Elizabeth died in 1579, and Napier then married Agnes Chisholm, with whom he had ten more children.