The Nids could eat the Exatari, it's just that your biomass is problematic to work with compared to other species. The Nids will consider Exatari to be more mobile ore nodes than true species, so useful but not less so than organic matter. I will say that the Hive Mind is going to more or less ignore your warp shred, that is fairly condensed localized to the Exatari in general.
The Hive Mind if it tried to connect to an Exatari would find 0 success but just controlling other nids wouldnt be impacted. Although, the one upside is that genestealers can't work on Exatari. Your reproductive system is too different and impersonal to tamper with, to not consider the whole part where the Hive Mind cant link to Exatari period.