.....although yes, it is not uncommon for monasteries to cover the face or even the whole image of the Protector, even in their protector chapels. I have seen this in Phelgyeling, and various other DS monasteries, for example.
This is also because the practice is generally considered to be of a tantric nature. By right, we should not even openly talk about having the practice as it is secret in nature.
Also, in general, images of wrathful deities, including deities such as Vajrayogini, Yamantaka etc were traditionally not revealed to the uninitiated, precisely for the reasons that you had mentioned, which are that people may develop wrong views if they do not understand the reasons behind their wrathful appearance, nakedness etc. and perhaps even put them off the practices for all the wrong reasons.
Nowadays, many lamas do openly show the images of these deities as there is usually teachings and explanations to go along with it. Also, it is by the many lamas' kindnesses that we can even see these images, for karmic imprints to be imprinted onto our minds. Not many of us will engage in very deep practice in this day and age, so the Lamas work another way by planting as many images of the Buddhas as they can in our mindstreams, that they may open up at a later time when we are more able to practice.
