What P-1609 meant, I assume, is why would Prometheans have an EMP Grenade in the first place if all their other weapons were used to combat the flood. If you recall, all known Promethean weapons have a disintegration effect to stop the flood from spreading. I assume he just thought it was odd that a force using heavy anti-flood weaponry would use an EMP Grenade. But I guess Tallgeese answers that question!