Suggest you read the following paper to understand the basic background of using pseudopotential for the calculation of NMR, Electric Field Gradient (EFG), and so on:
http://www.tcm.phy.cam.ac.uk/~jry20/gipaw/emr.pdf" what does the quarupole moment calculated through ATK signify?"
It is calculated only by taking into account the charge density of valence electrons of whole system.
The reliability of the use of only the valence charge density for the EFG isn't high. Additional contributions should be taken into account, as discussed in the above reference.
In the reference paper as you mentioned, the nuclear quadrupole resonance was calculated by the Gaussian code, which explicitly treats the core electron density.