We have carried out detailed bulk and local probe studies on the hexagonal oxides Ba3MIr2O9 (M=Sc,Y) where Ir is expected to have a fractional oxidation state of +4.5. In the structure, Ir-Ir dimers are arranged in an edge shared triangular network parallel to the ab plane. Whereas only weak anomalies are evident in the susceptibility data, clearer anomalies are present in the heat capacity data. Our 45Sc nuclear magnetic resonance (NMR) lineshape (first order quadrupole split) is symmetric at room temperature but becomes progressively asymmetric with decreasing temperatures. This is suggestive of distortions in the structure which could arise from progressive tilt/rotation of the IrO6 octahedra with a decrease in temperature T. The 45Sc NMR spectral weight shifts near the reference frequency with decreasing T indicating the development of magnetic singlet regions. Around 10K, a significant change in the spectrum takes place with a large intensity appearing near the reference frequency but with the spectrum remaining multi-peak. It appears from our 45Sc NMR data that in Ba3ScIr2O9 significant disorder is still present below 10K. In the case of Ba3YIr2O9, the 89Y NMR spectral lines are asymmetric at high temperatures but become nearly symmetric (single magnetic environment) below T~70K. Our 89Y spectra and T1 measurements confirm the onset of long range ordering (LRO) from a bulk of the sample at 4K in this compound. Our results suggest that Ba3YIr2O9 might be structurally distorted at room temperature (via, for example, tilt/rotations of the IrO6 octahedra) but becomes progressively a regular triangular lattice with decreasing T. The effective magnetic moments and magnetic entropy changes are strongly reduced in Ba3YIr2O9 as compared to those expected for a S=1/2 system. Similar effects have been found in other iridates which naturally have strong spin-orbit coupling (SOC).