A simplified treatment which uses just a fixed terrain height threshold would be dead easy to do. The main problem would arise for any map which has largely 'smooth' topography but a high general land elevation.
In my view, low level (i.e., within some depth above ground level) shear should be confined to more rugged terrain, not simply be tied to terrain height by itself.
One work-around would be to create a new map load.ini entry which specifies for that map whether shear should be invoked or not. For example, a load.ini containing a line like
WIND_SHEAR_ENABLED
would enable the application of shear when the plane is over terrain of a set elevation and when the plane is below the height threshold over ground.
An additional degree of control could be afforded by altering the former load.ini entry to
WIND_SHEAR_GROUND_HEIGHT 400
This would simultaneously enable shear and set the terrain height lower limit over which it is active. Here, only when one is over terrain at an elevation of 400m or higher will shear be experienced. If the load.ini has no such entry, shear is disabled by default.
The advantage here is that it can better accommodate the differing terrain among maps. For maps having mountains of considerable height, or if the lower elevations are already at no small height above sea level, or if most of the map is at or near sea level and only small parts are mountainous, the shear threshold height could be raised so as to best harmonize with the map's disposition of terrain.
And so an effective two-part control, which enables/disables AND allows to fine-tune a height threshold for a given map, would go some ways toward an invocation of shear which does comport, to some small degree at least, with physical principles.