Like someone has said, people don't really think about it that much. No one is out there saying we should "conquer the world like we did before", but they do look at that as the "greatest period in our history" and they praise our "courage" for "finding new worlds". Portuguese people were the discoverers, it's like the world is what it is because of our amazing courage and abilities[1]. The fact that we did that while pillaging, murdering and raping is often not even considered.
It does not help that we have "Os Lusíadas" which is a literary wonder in terms of its form, but whose content is basically emphatically praising those times. I hate "Os Lusíadas" not due to its form, like many young people do, but due to its content and how it praises the story of how we went about being warmongers and rapists.
So while you say that people "rationalize", most people really haven't thought about it at all.
[1] We're one of those countries that are so small or have such an inferiority complex that we are obsessed with anything in the news or history of the world that involves us. We go crazy because Obama's dog is a "portuguese water dog", or because "Cristiano Ronaldo" is well-known, or because some character in a sitcom mentioned us. So knowing that we were once "great" or "responsible" for something usually fills us with never-ending pride. I can't get this mentality, and I very much despise it. I guess it just shows how disconnected I am. I love our people, and I think we're genuinely nice, polite and have decent work-ethic, as well as a country with reasonably beautiful landscape, a safe environment and nice weather (not for me, but for most people). However, that's about it. In other words, if a war broke out and I had to choose between leaving the country or fighting for it, I would definitely not fight for it, as it means very little to me. There are many things that mean much more to me than my country, and those I would be willing to fight for.