We present synthetic dust polarisation maps of 3D magneto-hydrodynamical simulations of molecular clouds before the onset of stellar feedback . The clouds are modelled within the SILCC-Zoom project and are embedded in their galactic environment . The radiative transfer is carried out with POLARIS for wavelengths from 70 \mu m to 3 mm at a resolution of 0.12 pc , and includes self-consistently calculated alignment efficiencies for radiative torque alignment . We explore the reason of the observed depolarisation in the center of molecular clouds : We find that dust grains remain well aligned even at high densities ( n > 10 ^ { 3 } cm ^ { -3 } ) and visual extinctions ( A _ { n } { V } > 1 ) . The depolarisation is rather caused by strong variations of the magnetic field direction along the LOS due to turbulent motions . The observed magnetic field structure thus resembles best the mass-weighted , line-of-sight averaged field structure . Furthermore , it differs by only a few 1 ^ { \circ } for different wavelengths and is little affected by the spatial resolution of the synthetic observations . Noise effects can be reduced by convolving the image . Doing so , for \lambda \gtrsim 160 \mu m the observed magnetic field traces reliably the underlying field in regions with intensities I \gtrsim 2 times the noise level and column densities above 1 M _ { \sun } pc ^ { -2 } . Here , typical deviations are \lesssim 10 ^ { \circ } . The observed structure is less reliable in regions with low polarisation degrees and possibly in regions with large column density gradients . Finally , we show that a simplified and widely used method without self-consistent dust alignment efficiencies can provide a good representation of the observable polarisation structure with deviations below 5 ^ { \circ } .