In general, the choice of grammatical aspect is, unlike tense, not strictly delineated. You can often choose between two or more aspects to express the same basic idea, because aspects have less to do with denotation, and more to do with connotation. In other words, aspects carry implications and tonality, but they have less effect on the literal meaning of the sentence. As a result, the "correct" aspect is often a matter of opinion and interpretation.
So, let's go through these examples:
John hasn't studied very well this term.
This is present perfect simple, as your book says. It carries the connotation that John's poor study habits are either already causing problems for him, or are likely to cause problems in the near future. For example, you might continue the sentence like this:
John hasn't studied very well this term, so now he's at risk of failing the exam.
The emphasis is on the consequences of the action, even if those consequences are not explicitly stated.
Now, let's look at your other example:
John hasn't been studying very well this term.
This is present perfect continuous. Since it's still a perfect aspect, it still conveys the same emphasis on consequences. However, it also suggests that there is still time for John to change his study habits. It sometimes shows up in cases where the action is interrupted or altered, as in this continuation:
John hasn't been studying very well this term, so the teacher gave him an extra assignment.
We could also have something like this:
John hasn't been studying very well this term, but he could still catch up.
These continuations are (for the most part) also possible with the simple perfect, but they make more logical sense in the context of the continuous perfect.
Having said all that, you generally cannot use the present perfect continuous in cases where the action is far in the past, or otherwise "complete." Similarly, the simple perfect is usually considered less appropriate for a continuous action which is still ongoing (although, as in our examples above, it can sometimes be used with habitual or repeated actions, especially when those actions are unlikely to continue).
Best Answer
Your sentence is fine. It is very precise, and the style of writing that comes with graphs usually requires such precision.
The revised sentence is bad. I'm concerned with this part:
The word both is being used to introduce a set of parallel elements. But they are not parallel. The first is number of shops. The second is those. For the structure to be parallel, the word that fills the slot occupied by those must be filled with something equivalent to number, not something equivalent to shops. The use of those also fails because it does not match saw large fluctuations. The shops did not see fluctuations. The number did.
You could write the sentence this way:
But your original is better because the word both unambiguously signals the boundary between the grammatical subject and its verb.
You could also write your sentence like this:
This might be better if you want your reader to think about the numbers separately. I like it a little less, however. Although number is technically singular, it has a plural feeling. To me, both sounds more natural.