This may be an intentional balance thing, but I've found that missiles hitting during cloak and during stasis behave differently.
During cloak, it appears they are neither counted as hits or misses and do not reduce enemy EVA at all. This seems likely to be the intended functionality.
On the other hand, when missiles hit a stasised room, sometimes eva is reduced by the full tracking amount and sometimes only half. So it seems that the calculation for whether the missile hits gets run to determine tracking, but then the damage/effect of the missile is blocked by stasis.
It's unintuitive that cloak and stasis affect missiles/tracking differently, and stasis doesn't even default all missiles to "misses" because sometimes they only do half tracking which is a characteristic of a "hit."