That is true for most things in the cell, though. There's an incredible amount of redundancy, optionality, and just plain unnecessary stuff. Vaults stick out because they're an apparently unnecessary thing that you can see down an electron microscope. There are many more equally unnecessary things that are just a lot smaller!
I'd like to point out that any protein that is produced takes up precious resources. Our evolutionary intuition suggests that unnecessary things should be dropped from the genome.
Suppose a protein is unnecessary. Then there would be no evolutionary pressure to keep it from mutating and loosing its function(and mutations happen all the time!). The organisms would just gradually loose it to mutations and we wouldn't find a conserved protein throughout eucaryotes. So there must be something keeping it.
One conserved over the whole tree of life? That's like imagining an editing bug that Emacs and Vim have both carefully and inexplicably preserved from the last universal common text editor.
The genome is full of retrovirus remnants, so there’s a way for a parasite to piggyback on the host genome. Alu repeats in human genome are one such example. But there’s a hypothesis that these get “domesticated” by the genome and start serving a function.
