Jacques, I am inclined to agree with your observation that the use of "de" varies by country. And your post seems to suggest that wikitree should include "de" for medieval generations of families that later dropped the particle. (I'm not sure if that's what you really meant. My understanding is that there is a technical point related to wikitree searches that affects this question, but perhaps the system has been or could be changed.)
However, your examples of the Clare and Beaumont families don't seem to be relevant to the discussion at hand. The Clare family died out in the medieval period, when the "de" prefix was in universal use, so it's not good example of anything. And the Beaumont family is a good example of a family that DROPPED the "de" in later centuries -- the opposite of the De Vere family. If you could provide an example of the use of "De Beaumont" in the 17th (or even the 16th) century, that will force me to reappraise my point of view.
Your dismissal of my reference to Edward De Vere (d. 1604), the 17th Earl of Oxford, shows that you missed my basic point. I will reiterate for your consideration:
1. Aristocratic English families dropped "de" from in front of their family names as the medieval era gave way to the Renaissance, in the general period of the 15th century.
2. A notable (and apparently unique) exception to this was the De Vere family.
3. A famous example of this notable exception is Edward De Vere (d. 1604), the 17th Earl of Oxford. His enduring fame is derived from the well-argued claim that he was the author of Shakespeare's plays. In other words, this Renaissance man's family name continues to be known as "De Vere," not "Vere," so it makes sense for wikitree to follow this usage.