Is the list of the twelve nidanas late?

Yes, this is very good point indeed about the books, the collections of suttas: Nikayas/Agamas.

According to Ven. Yinshun, Saṃyukta-āgama/Saṃyutta-nikāya was at first not being termed as nikāya or āgama, but generally named as the ‘Connected Discourses’ 相應教 Saṃyukta-kathā .

See:

About the term Saṃyukta-kathā, see p. 899, note 21 in “Ācāriya Buddhaghosa and Master Yinshun 印順 on the Three-aṅga Structure of Early Buddhist Texts” (2020) by Choong Mun-keat.

Calling the Saṃyukta/Saṃyutta discourses as āgama/nikāya ‘collection’ was until when the other three nikāyas/āgamas (MN/MA, DN/DA, AN/EA) were gradually developed and expanded from it (相應教 Saṃyukta-kathā) (Cf. pp. 10-11 in Choong Mun-keat’s Fundamental Teachings of Early Buddhism (2000)).