For instance, the UK has 278 place names containing the word 'Saint', out of a total of 51596 (Source). Germany has 148 places beginning with 'Sankt' (Source, there's no way of finding out the total number of places listed in the database without having to go through each place one-by-one, but I assume we're looking at a similar number of places in total). France on the other hand has 5042 out of 36658 communes containing the word 'Saint' or 'Sainte' according to the Insee, and I imagine the percentage of places in Spain or Italy containing the word 'San' would be fairly similar.
Is there a reason for this? I assume most places in Europe were named long before the Reformation so I'm not convinced it's a Catholic/Protestant divide, and besides you don't get that many more places with the word 'Saint' in it in Ireland or Austria.
Your search is a little bit too simple.
The german word for Saint is "Heiliger", if you search for "heilig" in the database of german city names you will get additional results. To make it even more complicated, while Sankt may the "official" version of the latin word sanctus, it may be spelled and written different in documents. I know this at least true for Annaberg-Buchholz (the towns name today), that was listed as "santt Annabergk", "sandt Annaberg" and "Sant Anaberg" back in the 16th century.
Also keep in mind, Germany of today just exists since 1989. St. Joachimsthal was renamed to Jáchymov in 1945 and is now located in the Czech Republic.
I can only address this with respect to Britain. However, I will say this, with respect to it:
Adoption of Latin loan words (such as "sanctus") into the vernacular was extremely rare, as far as we can tell (accepting that discussing the unwritten vernacular is always rather risky in this sort of context), during the Old English era which gave us most of Britain's best known place names.
Use of "sanct" in the written corpus is well attested (e.g., consistently, in Ælfric's Life of St. Edmund with respect to Benedict and Edmund and in the Old English Lives of St. Margaret, with respect to her - of which latter I can locate no digitised text). But the vocabulary used by monastic scribes fluent in Latin and the language used by the common people were not always one and the same. Latin loan-words are used quite rarely, and with no particular consistency, consequently, before the 12th century. We can garner from the fact that "Sanctae Marian sunu", "Sanctus Petrus" and "Sancta Margareta" are identified in this manner (i.e., preserving Latin inflections), in the Lives of St. Margaret, that what is being used is not an Anglicised loan-word, but rather merely a Latin name and title, inserted into an otherwise English text.
The upshot of all this is that I believe it profoundly unlikely that your average 9th century East Anglian would feel compelled, even were he inclined to name a place after St. Benedict, to name it after Sanct(us) Benedict, as this was not Benedict's title, to the extent that he had one, in his language.
Note that we do not encounter the word "sanct(us)" with respect to any of the apostles in The Fates of the Apostles. Or in Ælfric's Catholic Homilies, save in a single untranslated Latin phrase ("Annuntiatio Sanctae Mariae").