Although it may offend our aesthetic sensibilities, evolution frequently removes parts of an organism that aren't paying their way. It will do this even if the result is what we would judge to be an inferior organism. To clarify, let's look at an example completely tangential to the hepatitis D virus.
It is well known that there is a 'window period' during which we optimally learn a language - namely, the first few years of childhood. Of course, it is quite possible to learn a language later on in life, but the process is much harder and much less perfect. Why is this? Why would the brain so quickly lose what would seem to be a massive asset? Steven Pinker, in his brilliant book The Language Instinct, answers as follows:
The genes, shaped by natural selection, control bodies throughout the lifespan; designs hang around during the times of life that they are useful, not before or after. The reason that we have arms at age sixty is not because they have stuck around since birth, but because arms are as useful to a sixty-year-old as they were to a baby.
This inversion (an exaggeration, but a useful one) flips the critical-period question with it. The question is no longer "Why does a learning ability disappear?" but "When is the learning ability needed?" We have already noted that the answer might be "As early as possible," to allow the benefits of language to be enjoyed for as much of life as possible. Now note that learning a language - as opposed to using a language - is perfectly useful as a one-shot skill. Once details of the local language have been acquired from the surrounding adults, any further ability to learn (aside from vocabulary) is superfluous. [...] So language-acquisition circuitry is not needed once it has been used; it should be dismantled if keeping it around incurs any costs. And it probably does incur costs. Metabolically, the brain is a pig. It consumes a fifth of the body's oxygen and similarly large portions of its calories and phospholipids. Greedy neural tissue lying around beyond beyond its point of usefulness is a good candidate for the recycling bin.
(Wasn't that masterfully explained?) So, one helpful way of looking at the bits of organisms is to view them as a trade-off between their costs and their benefits. If some new innovation (or 'old' innovation, as Pinker shows) is too costly, it will tend to be removed by natural selection even if the new innovation made the organism 'better' in other ways.
And so to hepatitis D. This RNA virus is actually unable to replicate itself, which makes it a rather odd inhabitant of the microbiological world. You don't need to understand much about evolution to realise that an 'species' that can't replicate its genetic code isn't going to be around long. Yet, hepatitis D virus (HDV) is clearly still with us. What's going on?
It turns out that Hepatitis D piggy-backs on some of the machinery brought by hepatitis B when it infects liver cells. Without hepatitis B coinfection, HDV it is utterly helpless. Now this is often perjoratively described in textbooks, which cruelly label HDV 'defective', 'degenerative' or even, in echoes of Hitlerian narrative, as 'subviral'. But by now the opposing view should be clear. Far from being in some way the runt of the litter, HDV may equally be seen as the cleverest of the hepatitis viruses, since its enslaving of hepatitis B obviates the need to carry all its own heavy replication machinery.
It's a nice inversion of vantage points, I think.