Rhinoman.....it seems like you may be talking about a different type of dowel than what D is. The dowel he is talking about would not help very much, if at all, if the flywheel bolts would come loose (which should never happen, if they are red lock-tited and torqued properly).
D.....the only purpose for that dowel is to serve as an "alignment" dowel when installing the flywheel. If you lined up the holes, then you are good to go.....the dowel is definitely not used to hold the flywheel in position, if the bolts were to come loose, or completely out.
I would guess that the dowel was either taken out by a PO, or it had fallen out (it just slips in the hole, not a press fit, by any means)....there is usually enough oil seeping in that area that it shouldn't rust off.