I'm having the same issue.
To add a little more detail, after getting a notification, I had to unsilence the user in order to be able to see their comment below my chost. Then I re-silenced them.
Re-silencing them then cleared out the notification from my notification feed, but I would rather have not received the notification about their comment reply in the first place, or if I were going to receive a notification, to be able to click through directly from that to the comment reply they made, without having to unsilence them to see it.
We are having the same problem.
Someone we silenced replied to a comment of ours. We get a notification with the contents of their comment, but when we visit the post itself, it's not visible.
This is not sensible behaviour. We silenced them, which means we don't want to get notifications from them. At the very least, the notifications should be spoilered or in some "muted" category. If you intend to show a notification (spoilered or otherwise), the comment on the page should then also be behind a spoiler.
We have people silenced because we don't want to see _them_, but we don't care if they see _us_. Otherwise we'd block them.
Eden
example:
6 people have this problem