SE hides comments with low or no upvotes in long discussions to prevent the comment section below a post from getting too long and the user having to scroll to see the next post.

This is usually a good idea, given that many comments do get ignored and just don't deserve as much attention as other comments in the thread. There's no point of including them in the default view.

However, some comments don't get upvotes because the majority of the community does not agree with them. These kinds of comments would probably get downvotes, if it were possible.

Comments like these will typically be part of a debate and be followed by a reply that has tens or hundreds of upvotes. However, because they have fewer upvotes than the other comments, they're hidden and the replier seems to be replying to nothing. In order to find out what the reply was about, you need to scroll to the bottom of the post and click on View All Comments.

I think there's absolutely nothing wrong with removing comments that violate guidelines. (therefore, this question is not a dupe of Comment removal and subsequent flow of discussion issue). However, if it's just a disagreement, then hiding these comments can actually require more scrolling for the reader, and not less.

I propose that comments in discussions should not be hidden, regardless of how many votes they do or do not have. Only comments whose author is not mentioned in the following comments should be hidden.

I know this is a minor thing, but it's also an easy fix.