Can I use 2 guidance chips modifications e.g. on a kihraxz?

No because Kihraxz says 'three *different' modifications'.

I doubt there will ever be a way to equip multiples of the same modification, but if in theory there were, you would be able to equip multiple Guidance Chips, and use each on one missile/torp attack.

Ah yes right I forgot. Thx!