Onyomi vs. Kunyomi?

Generally, words that could be written in Kanji but aren't are written in Hiragana. For example, Suizokukan (aquarium) would be written as すいぞくかん normally rather than スイゾクカン. Btw, the kanji is 水族館. This word is used because the on'yomi of In real Japanese sentences, katakana is reserved for foreign words not of Chinese extraction. Occasionally, some people might write names in katakana, particularly if the person prefers it that way or if they're being cute, but that's an exception.

Now, what you saw is actually common, and used to differentiate on'yomi and kun'yomi further. Basically, to emphasize which one is the native Japanese and which one came over from China based on a visual cue. Trained eyes would look for which system is used, and hopefully have an easier time encoding that information into their memory. Since it's hard to keep them straight sometimes, the idea is that it'll help the brain make further distinctions. For example, 水 would have みず and スイ (mizu and sui, kun- and onyomi respectfully) as potential readings in a dictionary explaining the kanji but in sentences where you'll find 水 as sui, すい would be used instead of スイ (if failing to use the kanji, that is).

Now, that's ONLY when differentiating between onyomi and kunyomi in a dictionary. In real world sentences, USE HIRAGANA!