Comments with high scores seem to have slightly higher scores than they would have, but comments with low scores seem to have about the same. Probably because the -4 limit on displayed comment scores was already concealing the actual score.
People don't know if it's at +5 or +500 so they might be more likely to click the upvote on a comment that's already got plenty of karma.
Next, a high quality comment need not have comments. Some of the best comments do not need followup. We should also discourage comments that merely parrot the parent and offer no content of their own. This is probably the biggest argument I have against not having any soft of indicator. If a comment is good, it deserves an up vote to indicate quality.
Next, replies still do not solve the scanning problem. For me to deduce the quality comments using replies requires I read through all the comments. Sometimes this is not an issue, but posts with a larger number of comments, this becomes problematic.
Finally, the above also means that replies of comments, and replies of replies, suddenly makes it really difficult what others deem quality content.
At the end of the day, up voting comments is meant to distinguish good, high quality comments from the normal run of the mill comments. If it's not being used for that, then up votes are merely being used as a way to obtain karma. In fact, I'd go so far as to say that by removing karma from showing which posts are of higher quality, it serves no real purpose other than to obtain more karma. I'm more interested in reading quality comments than obtaining karma, something the current system doesn't assist with. It only makes karma something to "brag" about.
FWIW: I like the comments with hidden scores better than before.
The value of the points on comments before was to help distinguish higher quality comments. Comments that added value generally got a higher score, and we could browser for that.
That can no longer happen.
By all means do not display the points on comments, but do not remove the ability to scan for higher quality comments. You can use some other visual method or indicator to suggest that certain comments are higher quality.
Otherwise, the karma does nothing except provide an encouragement to post comments and links so you can get karma...? I just don't see the value.