No, clip brushes shouldn't make the model disappear. If the models origin is inside a wall, it will cause the model to disappear, if the models origin is way off from the model, it will cause the model to disappear.
The model is only drawn if the "engine" can see the models origin. Its hard because on some models, the origin is in an unusual spot. When you click on the model in hammer, the red x is the models origin, make sure that is not inside a wall.