There isn't really any such thing as clutter and typically the size issue is a moot point. You'd be talking a couple of MB in most cases.
Whatever has caused your thread_id to no longer be equal to your number of threads is going to be a completely expected behaviour.
It may even be hard deleted threads. It may be that you have set the option on some forums to not include the threads in the board totals.
So, really, whatever it is, it doesn't matter and not likely something you can change, nor is it indicative of anything wrong. It is what it is.