Downside of doing that (at least in Connect), is that it will block comments from users on those instances as well. I blocked a few furry instances because I'm not interested in that stuff, but it ends up blocking quite a few innocuous comments in random threads. It's less of an issue with the explicitly NSFW instances though.
If you block an instance through the Lemmy UI directly, it only blocks all content posted to those instances. If a user from the blocked instance comments or posts in a community on a different instance, it’ll still show up for you
In Connect there's a "Blocked Instances Includes Comments" checkbox in your settings to block or show comments from blocked instances, under the Block List section.
My experience on Connect is that it puts up a "spoiler"-like filter on comments from users on blocked instances, giving you the choice in the moment of whether or not to reveal it. Super useful for blocking hexbear posts and giving me control over whether I choose to see hexbear user comments on posts on other instances
True, I don't like seeing hexbear posts but as long as the conversation isn't too political I don't mind seeing their comments in other threads. I like Connect's system
Yeah, you can click to show, so it's not a huge obstacle. Still, I'd rather just have the option of showing them from certain instances, but I get that that would be a lot of work to manage.