Is there any reason behind the ghost reputation we gain on the meta of a Stack Exchange site? This reputation doesn't add up to anything, but it still shows me I have gained some. Is this supposed to make any sense?
From the FAQ of any of the child metas:
This has a couple of consequences:
So, you may not be earning the reputation points that it shows, but it is still an indicator of activity. Don't you want to know when you get an upvote? You just need to think in terms of what each value of reputation points gain/loss means in terms of vote activity.
You can also earn badges on the meta site that are independent of badges from the parent site. Mortarboard is the first example that comes to mind relating to your reputation points. Other badges like Good/Great Question/Answer, etc. relate to upvotes. In the Stack Exchange system, votes tie to reputation points. A side effect of it being the same code-base, but I don't see it as a big enough deal that it would warrant changing for the meta sites.
There is also a blog entry that discusses the per-site metas.