So, it seems that with regards to chemistry the normal trend is followed: true Japanese words are written in kanji or hiragana while foreign words that must be borrowed are written in katakana. This is clearly out of simply necessity. No one can blame the Japanese for not having a traditional word for elements or compounds not discovered until the 20th-century, and, anyway, coming up with their own words and kanji for all these chemical species would be impractical at best and impossible at worst.
In another example, in a book in the manga series クレヨンしんちゃん (aside from the obvious loanword usage in the title) I found an example of the onomatopoeia キキッキ, used for laughter. I actually find this to be an example of a case where the use of different writing systems in Japanese is actually able to draw a relevant distinction, because onomatopoeia are fundamentally different than other words in English, yet have no obvious distinction in the written or spoken language. While "normal" words represent an abstract concept while remaining distinct from it, onomatopoeia such as meow are an imitation of that exact concept. It is an interesting distinction that I am sure Japanese people are much more aware of than other Westerners because of the use of katakana for onomatopoeia.
In looking at the textbooks' explanations of katakana, I actually found remarkable consistency. Some left out the onomatopoeia aspect of the katakana, but that does not surprise me as that is relatively minor when it comes to overall usage. Especially when it comes to a foreigner attempting to learn Japanese, the use of katakana for loanwords is much more relevant to learning Japanese.