"Here and there were tents" would be the typical phrasing. That is a phrase which indicates that there are many tents, though there is typically no visible structure to them. That can be contrasted with "a long row of tents" which has a very clear row-like structure. Those phrases together would show a well ordered group of tends (in a row), of which some portion are "obviously magical," but there's no particular rhyme or reason to it.
Rowling's choice of "Here and there was a tent" is a more atypical phrasing. She is using an unusual construction which gives more of an impression of isolation. The magical tents are kind of independent, each one standing on its own.
I would read into her words as an explanation for why Mr. Roberts is merely suspicious. In his mind, each of these "obviously magical" tents is an isolated thing, and he hasn't yet connected the dots. He hasn't linked together all the information he's observing about each tent to come to a conclusion that the tents, as a whole, were magical. If she had used the more typical phrase, "Here and there were tents..." that would give more of the impression that the dots are indeed being connected.
Personally, I would almost always use the more typical plural sentence. However, a writer often understands the subtle effects word choice has. In this case, Rowling chose the singular.