In the following sentence, 最近、宿題をしてこない生徒が多いです which means "Many students come to school without doing homework." why doesn't this mean "Many students don't come to school or do homework." or even "Many students do homework and don't come to school"?
The negative in the sentence ない is used for the noun 宿題 homework hence the translation "Many students come to school without doing homework." is correct, not the other two.
If you are asking about the difference between "...ていく" and "...てくる", they are usually used as suffixes meaning "to go and do ..." and "to come and do ...". You should see this, this and also this to understand it better.
It never means "Many students don't come to school or do homework.", which would be something like 宿題をしなかったり来なかったりする学生が多いです.
- "Many students come to school without doing homework"
- "Many students do homework and don't come to school"
For these two, there are possible ambiguity, which is usually disambiguated by context and stressing (くる will be considerably weaker if in an idiom). Context always matters, because:
#3 would be more likely understood as #1, but #4 as "be sick and don't come". Ambiguity in parsing is common in every language, like in a classic example "time flies like an arrow; fruit flies like a banana", where the reader is expected to solve it with common sense.
In writing, a conscientious writer would feel putting a comma (宿題をして、こない) or making it kanji (宿題をして来ない) if they really mean #2, but this is totally optional.
FYI sometimes I think that Vてくる pattern is more appropriate to be translated "one has V-ed by (the time) one gets here", in terms of where the actual focus lies.