I might not have as much experience as you, but if I've only learnt one thing from being active on Reddit is that giving your personal karma-score any meaning is just a major headache and best be avoided. But the development you are talking about can also be witnessed there. For example in /r/programming, there used to be things such as posts with 91 comment karma and _0_ downvotes. This stuff doesn't exist anymore, the community has grown, become a lot less homogenous and more 'nay-sayers' have introduced themselves.
The above is of course just an example that is indicitative of what I'm talking about. In my opinion, it is best to simply accept downvotes without explanation as background noise. They happen and there's not much you can do about it.
I know what you're talking about but it doesn't apply to comments. The only thing that automatically adds up and downvotes to comments is what they call 'fuzzy comment karma' which is to prevent bots from figuring out too quickly that they have been shadow-banned, since to them it looks like they are getting 2 downvotes here and 3 upvotes over there.
The system has been active longer than the post was old and it's just and example, if you read through comment threads back then and now, you will notice the difference without having to rely on karmic metrics.
