How can Itachi's genjutsu act on Mecha-Naruto "Robot"?
Mecha-naruto can absorb and contain chakra. This could mean that he has some kind of a chakra system. he also has a eight-trigrams seal in order to seal kurama and this confirms the previous statement. This chakra would in turn be used by his chip for its functioning similar to how the brain uses electric signals flowing through the nervous system.

The chip could be thought of a mechanical brain that uses chakra(it can sense chakra too!)and gives you all reasons why itachi could use genjutsu on mecha naruto.