It seems to me that both mean the same thing, but which one is more frequently used?
They mean two different things.
Without も, the sentence would look like this.
B exists in A.
Two pieces of information are involved here.
In the following sentence, も works on the place.
B exists in A, too (= as well as in other places).
This puts Place A in the same category as other places where Object B exists.
In the following sentence, on the other hand, も works on the object.
B exists in A, too (= as well as other things).
This puts Object B in the same category as other things that exist in Place A.
も is not an adverb like “too” or “also” in English. It always works on the part that precedes it, and therefore, it cannot cause the kind of ambiguity the English words sometimes do.
Note that when the original particle is が, it is replaced with も, whereas when the original particle is に, も is appended to it.