how does it measure the frequncy of the port if it does not know the displacement of the sub?

since net volume plays a role in the frequency, it'll just calculate the port with the total net volume of the box. sub displacement will change the net volume slightly which will in turn change the net volume. i have never used the ssa port calculator, so i would either guess it takes out a set amount for sub displacement automatically, or just has zero in for sub displacement which i think is more likely

so i should be alright with the frequency i tuned it at then if it only brings it down a little bit

it is only a 1.2 cu ft box tho so will it be effected more

Sub displacement is usually so minimal, it won't change the sound noticeably.