Hey Auntie
The truth is, the only way I can differentiate between syllables is from context. And knowing Hanja would definitely be beneficial to my own Korean language education! I would love to be one of those old scholars that have long white beards with big black hats, walking around with an old Buddhist text written all in Hanja. But, I'm not there yet... hehe
But in all honesty, as a Korean speaker/student, there is not much need to know the actual Chinese characters. With the exception of a few when reading newspapers, which is an extremely high level, Hanja is pretty much obsolete in modern day Korea.
But you can definitely tell that Hanja is laced ALL OVER Korean. And even though certain words have similar pronunciations, I think it's still best to learn it from the sounds, because Hanja would be excessive to learn. As Taliana suggested, it is definitely part of the language, and should be studied at some point. However, the way we are gearing this Hanja PDF is for lower intermediate and up, when learning the "hanja sounds," are relevant to Korean language education, and not necessarily the Chinese Characters (although we will be be including these in the PDF's as well).
I don't know if I made any sense with that
I need more sleep. haha! I'm not sure if I answered your question, but, as always, feel free to ask again!