Is this intentional? It had me confused for a while.
I think it's intentional yes.
Thinking about this, random people checking merits aren't going to know what the thread is where a post got merited, but you will/may know the exact part of the thread you got the merit from. If not, going to an archive site that archives this forum regularly and checking the link there will give you waht it was merited for (providing it was archived after the merit was given).
This explanation doesn't make sense, particularly since when the OP looks at the merit lists for other people he's getting an error for the thread link...because the thread no longer exists.
To the OP, I bet your posts for which you've earned merit aren't deleted, they're just archived. So they still exist on the forum, which is why you don't get an error when clicking on the link.
Forum system logic is...simple...and logical. It's not written to have random exceptions without a very clear and meaningful functional purpose.