It appears on first reading that "lots of paper" should be understood as a plural noun (lots) modified by an of-genitive "of paper". However a better analysis would be that "lots of" is a determanitive phrase, with a similar function to "some" (similar function but different meaning)
He used some paper ...
If you have a countable noun, you can say (for example) a lot of things or (less formally) lots of things. Whichever you say, the pronoun is then they.
If you have a mass noun, you can say a lot of paper or (less formally) lots of papers. Whichever you say, the pronoun is then it.
("Paper" can also be countable in some cases, but that's ...
This is a case where what is actually being talked about is multiple, but we are using a word that takes singular forms ("paper" is uncountable, but it takes a singular pronoun). The singular is technically correct, but there's some leeway to use the plural. BrE has more of a tendency to use the plural in these cases. You can also say "He used ...
If we use the term our usual way, yes, there is one sky.
Cambridge Dictionary, however, also has this definition:
skies [ plural ]
the sky in a particular state or place:
For weeks we had cloudless blue skies.
We're off to the sunny skies of Florida.
Ngram shows also significant use of 'skies'.
We may deduce that it is countable.
"Code" in the sense of "computer code" is a mass noun, and so has no plural. It would be "lines of code".
code .... Computing mass noun Program instructions. ‘assembly code’
... ‘The answer is 609,000 and this is the number of lines of code in the software for the computers and avionics systems.’ (Lexico - https://www.lexico....
It's all about the sense implied. In the first sentence(I hear a noise.) noise is synonymous with a sound. In this sense, the word refers to a distinct (loud) sound that can distract the mind for a short moment.
We say: 'Don't make a noise, please.' ['Please keep quiet.] Here, the word refers to a noisy atmosphere (as in a classroom) created by talking.