How can I know when to use Hanja over Hangul, or vice-versa?
Answers giving a bit of history/thorough explanation would be greatly appreciated.
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Out of 510,000 words listed in Korean Standard Dictionary published by National Institute of the Korean Language, approximately 290,000 words (57%) are composed of Chinese characters. However, it is very rare to see Chinese characters in Korean newspapers as not many Korean words are difficult to understand without reading their Chinese counterparts.
However, there are some words that are homonyms with different Chinese characters.
이사장 can mean either a president (CEO) whose family name is 이 (李) in '李 社長' or '理事長' (chairman of the board of directors).
연패 can mean either a consecutive win '連覇' or consecutive loss (defeat) '連敗'.
There are more examples where Chinese characters are needed side-by-side to make the meaning clearer. It is really difficult to tell the difference unless there is sufficient context.
I can imagine only these situations...
Usually, you have no need to deal with Hanja unless you are dealing with some very ancient stuff in Korea. Hanja is an almost completely dead system in daily life, and will decline more, and will likely disappear.
Though many Korean words (not all!) can be decomposed into some Hanja components, you don't have to memorize the shape of Hanja to decompose them. You can do it at a phonetic representation level, and that's what most Koreans do. Only old guys (over 50) have trouble distinguishing homonyms without Hanja. Younger people always prefer to provide more context.
I don't remember the last time I saw Hanja characters in any document, signboard, book or anything else. Most (especially younger) Korean people hate Hanja. Many people think it's useless, and that's why Hanja is declining.
Instead, what I see everyday is Hanzi or Kanji for Chinese and Japanese tourists. Not Hanja. These systems share many shapes, but have some differences in details because they diverged hundreds of years ago...
Pretty much never. Some newspapers use hanja to clarify homonyms (장기: 長期 long-term, 臟器 viscera, 將棋 Korean chess, 長技 specialty, etc.) but usually it's not hard to figure out the meaning through context.
It does help to learn some hanja, though, because you can sometimes figure out the meaning of a word by guessing the hanja. Also, some of the basic hanja is ubiquitous, so you should definitely learn to recognize them:
All the numbers, 日 (일 day), 月 (월 month), 年 (년 year), etc
小 (소 small), 中 (중 middle), 大 (대 big), 牛 (우 cow), 魚 (어 fish), 肉 (육 meat), 湯 (탕 broth), 正 (tallying), etc — common in restaurants