I tend to regularly find myself in discussions or read blog posts where it is suggested that dark themes are “easier on the eyes” and hence a better way to go. While a darker theme means that there is less light entering your eyes, in general a dark theme can cause more problems.
Most desktop themes are all light-coloured. This is not only true on Windows, but with GNOME and KDE. Furthermore, around 99% of websites at least have a light-coloured background as well. Now, when you have a large dark terminal open, or your own website theme which is dark as well, you will inevitably have to go to a new webpage frequently which is incredibly bright in contrast. Or, you might launch another application.
You might have a dark theme for your favourite desktop environment, but even so it is a lot harder to escape the majority of websites which are not dark. When you do end up launching such a website, the pupillary light reflex causes your pupils to contract very quickly. The amount of light entering the eye suddenly increases (even more so in darker conditions), and persistent occurence of this as a sudden transition can strain your eyes. This is not too dissimilar to going for a sprint without jogging first. For this reason a well-lit work area is just as important: that is, for when you look away from the monitor and back.
Now, I do not want to imply here that a purely white wallpaper, theme, or website background is ideal. A more ideal colour is one that is just off-white, to reduce glare which can also cause eyestrain and vision difficulties.
RSIBreak is also a nice application that helps you avoid repetitive strain injury.