Hello,
I have no idea of orders of magnitude of effect of horizontal density gradients, because we usually use Telemac-3D in such cases. I know it is important in the North Sea.
To get positive salinity you must use an advection scheme that ensures monotonicity: either characteristics (but not mass conservative) or distributive schemes : 3,4 5 or with tidal flats 13 or 14.
In case of tidal flats, make sure that you have:
TREATMENT OF NEGATIVE DEPTHS : 2 (and then follow instructions, Telemac-2D may ask other things like CONTINUITY CORRECTION=YES, etc.).
If you compute a tide on a large domain, 10 cm is the order of the accuracy we get on tidal range in the Channel, compared to measurements.
With best regards,
Jean-Michel Hervouet