I agree that it's a crude measure, but I don't think the situation is quite as bad as you make out; your intuition about paper libraries is misleading you.
What's being counted as a single item here is not a single bound volume of a chemistry journal, nor the entire archive of Bioconjugate Chemistry, but rather the entire chemistry-journals wing of the library: 539 gibibytes, including 226 different journals. By comparison, the latest five items on http://webcache.googleusercontent.com/search?q=cache:http://... are 3.7MiB, 11.7MiB, 350MiB, 730MiB, and 260MiB; the chemistry-journals library is some 2000 times the size of the median of these and 120 000 times the size of the smallest, which happens to be a two-volume book called "Great Moments in Mathematics".
It turns out that when you have a power-law distribution crossing five orders of magnitude, like the one that characterizes file sizes, rather than the much narrower distribution that characterizes book sizes, you actually can get a useful approximation of the makeup of the total by looking at the makeup of only the largest items. It's surely not an unbiased estimator, but it's still a useful one.
Feel free to invest the work to do a better approximation.