The fact that you say CV makes me thing that either:
1. You're in academia or some kind of research discipline.
2. You are not in the US (we distinguish between resumes and CVs, and CVs are almost unheard of in the engineering sphere here).
My comment about cover letters is US specific. Academic/research jobs should have a cover letter - I agree.
Most engineering positions I apply for do not require a cover letter - it is optional. If it is required, I do write one - but that is extremely rare. And I often do get calls from companies that allowed me to upload one (optionally) - even though I never upload one.
My guess is that the majority of companies that optionally allow you to upload one will never notice if you do.
My guess is that most likely the reason you can upload a cover letter (optionally) is that whoever designed the site is using a generic template - not because they actually want one.