We observe that nitrate ion has a trigonal planar geometry according to its lewis structure and the VSEPR theory. Its resonance hybrid consists of three contributing structure -three probable double bond organisations. According to my knowledge, we would expect that pi bond to be distributed equally over the molecule and thus, the dipole moments would cancel each other out. My question is, why such an ion would dissolve in water even though it is non-polar?
Don't overthink it.
The oxygens have a partial negative charge in nitrate from resonance. The protons in water have a partial positive charge from dipoles. Positives attract negatives.
Molecule polarity becomes an issue when discussing neutral molecules interacting with neutral molecules. Molecular polarity is one thing, and bond polarity is another. Transformations / arrangements / alignments of molecules such that the dipoles (the things that make a molecule or bond 'polar') align to maximize interaction are certainly important for dissolution, but when a species is a bona fide free ion, water will tend to dissolve it.