Ultimately the reason that we do commandments is because, G-d our Creator and King commanded us to do these actions, regardless of whether we understand or intuitively agree with the command.
His will is above our human considerations of morality.
However, it has been the custom of many Rabbis throughout the generations to try to find reasons for the commandments to make them more understandable to us.
This may be acceptable, so long as we don't say, that the commandment is no longer applicable because the underlying reason for it is no longer applicable. For G-d didn't make his commandments dependant upon our reasons and who says we even guessed correctly all the real reasons for the commandments.
With this in mind, I would like to ask the members of this forum what "reasons" do you have for the commandment to destroy the animals of Amalek.
To "start the ball rolling" I will at this time offer at least 3 possible reasons.
1] to make it clear to the people, that the war against Amalek is a national war, where we make absolutely no differentiation between Guilty Amalekites and Innocent ones. Such differentiations inevitably lead to Jews being killed. Liberals like to play Devils advocate and say, isn't this just like the Nazi treatment of the Jews in the Holocaust. My answer is that this is the wrong comparison. It's like the treatment the USA gave Hiroshima and Nagasaki with the atom bomb, which instantly ended World War II instead of having to fight with the purity of arms morality of the secular Zionists against Gaza which inevitably leads to losses on our side and possibly even losing the war altogether.
2] The Torah says that animals used for bestiality should be destroyed. By destroying the animals of Amalek we are declaring that we also suspect them of bestiality.
3] Perhaps there were hideouts of the Amalekites that would only have been found if we had completely destroyed their animals.