According to the American Heritage Dictionary of the English Language, fifth edition (2011), whitelist is spelled closed up both as a noun and as a verb, just as blacklist is. But that is merely one dictionary's judgment of where the spellings of the two words stand today.
The broader question remains, Why are some words spelled open while others are spelled closed, despite being composed of very similar parts? In AHDEL, for example, we find the preferred spellings black fly and whitefly. Why?
The answer is that orthography is not determined, first or last, by a centralized committee on consistent and rational spelling. The dictionaries may seem to play that role—and Noah Webster, for one, did seem to view his mission as a lexicographer in that light—but in reality they are in the business of reporting the preponderance of actual usage, not the form that is most consistent with other, similar spellings or with etymological analysis.
Terms come into use in different parts of the English-speaking world at different times, and their spelling is subject to further change as they become more familiar and more widely recognized. To some extent, they reflect related spelling conventions (so you wouldn't expect the spelling blakflie to catch on), but at some point the marketplace of users decides which form or forms will be dominant in writing—at which point the dictionaries simply report reality as they find it. For an example of this phenomenon you need look no farther than the entry for white list (rendered as two words) in the fourth edition of AHDEL (2000).
Especially as terms become more familiar to the readers, they become susceptible to losing letter spaces (if rendered initially as two words) or hyphens (if initially hyphenated). However, this is by no means a thoroughly predictable phenomenon either. For example, I have been expecting for at least twenty years that dictionaries will follow common industry (and some popular) usage and identify healthcare as the primary spelling of that term—but it still hasn't happened.