It's cheaper to write to the DB when doing ordering updates, but you lose easy 'order by sort_order' in queries since the nodes you're linking to will likely be primary keys that are in a different order than the creation sequence. This probably has index ramifications but I don't know enough about them to say.

That's fine if you sort everything on the front end though. It's product-dependent.

Like someone else said, usually these kinds of lists are small enough and PCs/databases are fast enough for it to not really matter.