TL;DR: The colon is a typographical error, not an early emoticon.
One way to investigate this kind of question is to use full-text search on a suitable corpus. For example, we could search the Internet Archive for nearby words, sorted by publication date and see which editions have the colon. (Note that some care is needed in interpreting the results, because the digitization process does not always capture an accurate publication date.)
A complication is that Wells wrote several versions of The Time Machine:
The earliest draft of the story was called The Chronic Argonauts and was serialized in the Science School Journal, the students’ magazine of the Royal College of Science, in 1888. It had only the bare idea of ‘time travelling’ and a few lines of dialogue in common with the later versions. Wells subsequently made two further drafts, which are lost, and early in 1894, in response to a request by W. E. Henley, he returned to the story and rewrote it as a series of loosely connected articles for the National Observer. The first of them appeared in March, and six more were published between March and June, but the series was discontinued after Henley gave up the editorship. These article have a fairly close resemblance to the story as we now know it, particularly the first of them, but contain only a fraction of the material. […] At the end of the year Henley took over the editorship of the New Review and arranged for the novel to be serialized
there: it appeared in five instalments from January to May 1895. At the end of May The Time Machine was published as a book by William Heinemann, and this version is still in print. It is largely, though not entirely, the same as that serialized The New Review. Some years later Wells made a few minor changes in the text, which mainly consisted of removing the chapter headings and running various chapters together; and this revised text was included in the Atlantic Edition of his works [1924]; it has since been reprinted in The Short Stories of H. G. Wells [1923] and the Everyman’s Library edition of The Wheels of Chance and The Time Machine.
Bernard Bergonzi (1960). ‘The Publication of The Time Machine 1894–5’. The Review of English Studies 11:41, pp. 42–43.
The 1895 text lacks the “(as we thought it)” parenthesis, which appears for the first time in the 1923 revised text. The following table gives a selection of editions of the 1923 version of the story, in date order.
You’ll see that the colon is missing from the early editions, and appears for the first time in the 1957 Berkley edition. (For the first time in this corpus, that is: there may be other editions for which the Internet Archive does not have digitized copies.) The subsequent appearance of the colon in the Bantam and Signet editions suggests that these two publishers copied their text from the Berkley edition (or all three copied it from a shared source).
