Why is "de" included in the former but dropped in the latter? Are there any general rules that determine this?
We usual use the whole last name as the formal way to go. This specific case (Francisco de Vitoria) is a weird example, I would never have called him 'Vitoria' but 'de Vitoria', being a native speaker myself. This is probably influenced by old Spanish uses, but that's not the rule nowadays. Just use the whole last name when speaking formally.