Here's one possible reason that you see words like pre-processing hyphenated less in scientific papers: the more familiar you are with a word, the less likely you are to hyphenate it. And scientists using technical words in scientific papers are more likely to be familiar with them than non-scientists using them in prose.
To illustrate that familiarity breeds non-hyphenation, it's a well-known fact that hyphenated words have a tendency to lose their hyphens over time. See this blog entry:
Sometimes, however, compound words that were once hyphenated become so familiar that we treat them as single words, like the word online. Newly formed compounds tend to be written first as separate words or with hyphens and gradually become unhyphenated as they find their place in our linguistic consciousness. ... Thus, the formerly hyphenated compounds bumblebee, lowlife, and crybaby are now spelled as single words.
Should you hyphenate words in a scientific paper? I don't think it matters one way or another—my advice would be to use the spelling that is most common in the research community who will read the paper, and don't worry too much about it either way.