I consulted several style guides to see how they recommended handling words that begin with various prefixes. To my chagrin, none of them addressed the specific prefix auto-. Nevertheless, they did offer general advice on how to handle prefix hyphenation that is readily applicable to auto-prefixed words.
The Oxford Guide to Style (2002) notes that "The hyphen is used less in U.S. practice" in situations where Oxford would endorse using a hyphen—as with the words noneffective, nonnegotiable, reelect, and reenter. It presents these guidelines for British English practice:
Words with prefixes are often set as one word, but use a hyphen to avoid confusion or mispronunciation, particularly when there is a collision of vowels or consonants:
re-entry, de-ice, anti-intellectual, quasi-scientific, pro-life, semi-invalid, pre-eminent, non-effective, non-negotiable, ex-directory, vice-chancellor
Although Oxford doesn't include any examples involving the prefix auto-, I would not be surprised if it endorsed the spelling auto-populate "to avoid confusion"—as it does in the case of non-effective. Admittedly, autopopulate doesn't involve a collision of vowels or consonants, any more than automobile does. But the stronger British inclination to include hyphens in unfamiliar prefixed words may be decisive in this instance.
The Chicago Manual of Style, sixteenth edition (2010) argues that words containing prefixes should be closed up unless they fall into one of five categories that would exempt them from the general rule:
Compounds formed with prefixes are normally closed whether they are nouns, verbs, adjectives, or adverbs. A hyphen should appear, however, (1) before a capitalized word or a numeral, such as sub-Saharan, pre-1950; (2) before a compound term, such as non-self-sustaining, pre–Vietnam War ... ; (3) to separate two i's, two a's, and other combinations of letters or syllables that might cause misreading, such as anti-intellectual, extra-alkaline, pro-life; (4) to separate the repeated terms in a double prefix, such as sub-subentry; (5) when a prefix or combining form stands alone, such as over- and underused, macro- and microeconomics.
Chicago goes on to exclude the prefixes e- (short for electronic), ex-, and quasi- from this general rule, but it doesn't mention auto- at all. I expect that Chicago would see no reason to hyphenate autopopulate, given that the word is in little danger of being misread.
The Associated Press Stylebook (2007) has this succinct discussion of prefixes:
prefixes ... Generally do not hyphenate when using a prefix with a word starting with a consonant.
Three rules are constant, although they yield some exceptions to first-listed spellings in Webster's New World College Dictionary:
—Except for cooperate and coordinate, use a hyphen if the prefix ends in a vowel and the word that follows begins with the same vowel.
—Use a hyphen if the word that follows is capitalized.
—Use a hyphen to join doubled prefixes: sub-subparagraph.
AP is very strict about its "do not hyphenate when using a prefix with a word starting with a consonant" rule—which is why the entertainment section of my local newspaper was using the spelling miniseries very early in the word's print existence; it took me some time to realize hat miniseries had nothing to do with miseries. In any event, AP seems to be firmly in the corner of autopopulate.
An older U.S. style guide, Words into Type, third edition (1974), indicates that the country's preference for closed-up prefix constructions was already well established 45 years ago:
Prefixes. The modern tendency is to eliminate the hyphen between a prefix and a root unless the root is a proper noun or adjective, such as un-American ... With common roots the following prefixes form solid words except on the occasions to be noted for homographs [such as re-collect an re-form] or when this would result in doubling a vowel. (Co-, de-, pre-, pro-, and re- may be set solid even when this forms a double vowel [as with preeminent and reevaluate].
The only prefix-based words that Words into Type identifies as being exempt from its general no-hyphen rule involve prefixes that end in a and attach to roots that begin with a: extra-articular, intra-abdominal, supra-auditory, and ultra-atomic.
As The Oxford Guide to Style notes, British publishing practice is far more open to including hyphens after prefixes that U.S. publishing practice is. I can easily imagine a British publisher going either way on the question of hyphenating or closing up auto-populate/autopopulate. On the other hand, it is now nearly a decade since this English Language & Usage question was posted, and the word autopopulate is surely familiar to many more people in 2019 than it was in late 2010. That being the case, the argument for including the hyphen in order to avoid confusion is considerably less compelling today than it was then. A similar line of reasoning would apply to other words containing auto-/auto as a prefix: the argument for including a hyphen may be strong when a word first appears on the scene; but as the word's familiarity grows, the rationale for hyphenating it weakens.
In the United States, meanwhile, major style guides have long presumed that a word starting with a prefix should be closed up unless it falls into one of a handful of narrowly defined exceptions to the general rule. Since autopopulate doesn't seem to meet the criteria for these exceptions, I would expect most U.S. publishers to close the word up—and to have done so even in 2010.