In the context given, the most correct and common way to say it would actually be
Stop being noisy.
Since they are already making noise.
Don't make noise.
Is correct, though it when used in that particular context it sounds a little strange to my (native, American) ear. If you were in a situation where you wanted to prevent future noise,
Don't make noise.
or
Don't make any noise.
would both be perfectly fine to use.
As far as noise being counted vs non-counted, the difference between 'noise' and 'noises' usually comes down to whether are multiple types or sources of noise. The difference between 'noise' and 'a noise' is usually whether the noise is sustained or brief.
For example, if there is a crowd of loud students in the hallway, you can say:
I hear a lot of noise in the hallway.
If there is a crowd students, and someone using power tools you might say
I hear a lot of noises in the hallway.
If the hallway is otherwise quiet, but someone loudly dropped a book it would be
I heard a noise in the hallway.
You could even use 'a noise' when referring to a sustained noise, though it would usually be coming from a single source, such as a dripping faucet, instead of a group of talking people.
Generally, because 'noise' is so flexible, whether you use 'a/any noise' vs 'noise' and 'noise' vs 'noises' the sentence will usually sound correct.
If I have some questions, I will write you is indeed less idiomatic than If I have any questions ... It's quite difficult to explain the difference formally (and of course, most native speakers would know this intuitively--in other words, they can use them correctly without much thought).
So, instead of trying to explain the usage of any and some systematically or formally, I will risk answering this question concisely, which could be more useful, by giving these paraphrases:
If I have some questions ... = If I have some amount/number of questions ...
If I have any questions ... = If I have any possible questions ...
And if you think about it, you may see that If I have some amount/number of questions, I will write you doesn't really work.
Best Answer
Only you know how you "do " understand it.
What you want to know is how you "should" understand it. Or, in other words, how most native speakers would understand it. Or in other words, what it means.