Convective cloud activity and rain squalls can have a drastic effect on the wind, but it is very difficult to ensure they are modelled in the exact right location, and with the correct timing. All weather models struggle with this problem.
The best method of estimating the impact of clouds on your average wind strength/direction is simply looking at them to judge their size, height, movement and proximity.
Convective Low Cloud: these can disrupt the local winds dramatically depending on how convective the cloud is. These clouds are usually 'fluffy' cumulus clouds and an extreme example is one that results in a thunderstorm. These clouds 'suck' air aloft,and if the cloud was directly upwind, you can expect the wind speed to be less before is passes overhead, and more after.
Rain squalls can also affect the winds in a dramatic way. These clouds 'push' air down to the surface, and so if the cloud was directly upwind, you can expect the wind speed to increase before is passes overhead, and decrease after.