According to Wikipedia,
NTP can usually maintain time to within tens of milliseconds over the public Internet, and can achieve better than one millisecond accuracy in local area networks under ideal conditions. Asymmetric routes and network congestion can cause errors of 100 ms or more.
The total time dilation effect experienced over a trip of distance D, at speed v, is
delta t ~ D/c v/c
This is the difference between the duration of a photon round trip between two observers, one fixed to the Earth and the other making the trip. Even for very large trips (say, an intercontinental flight of D= 10^4 km) on a fast jetliner (v = 1000 km/h), this only amounts to 10^(-7) seconds, which is way smaller than the accuracy aimed for by the NTP project.
Even for an interplanetary flight (D = 10^8 km, v = 10^4 km/h),the total error would be of order 3 msec.
Hence there is no need for any provision to be made within NTP for relativistic speeds. Such provisions are instead routinely made for interferometric observations as in the VLBI, or in accurate general relativistic experiments in space (see Gravity Probe B for an example) but this has nothing to do with what this site is all about.
For more info, I suggest you turn to https://physics.stackexchange.com/