In Heisig's book _Remembering the Kanji_ , 16th edition, kanji #519 (暗) is
named Darkness. In Yu-gi-oh however the darkness element uses 闇

According to the following link, 暗 does indeed mean dark, darkness. The same
site mentions the added meaning of gloom to 闇:
<https://jitenon.com/kanji/%E6%9A%97>

Why are there two kanji with the same basic meaning and how would I know when
to use one or the other?

Are there implied differences that can be inferred without actually explaining
by using one versus the other?
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meaning nuances kanji spelling
Kanji for darkness: 暗 vs 闇, nuance? meaning? use cases?
I can’t answer your question about “why” but there is a clear difference in
usage.

暗 means “dark”. In fact, it is the character for the Japanese native adjective
for “dark”, namely 暗{くら}い. When it is used as part of other words, too, it is
used attributively to qualify something as dark (“dark something”) whether it
is pronounced in _kun’yomi_ or _on’yomi_. Giving the noun form “darkness” as
one of the definitions for this single character could be a bit misleading. It
should be understood as the quality of being dark.

闇 refers to a place or situation where it is so dark you can’t see things
clearly, if at all. It corresponds to “darkness” in that sense.
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You would know which to use because they are used differently.

You don't actually use single kanji very often, so there isn't much confusion
(just like in English you know when to use "darkness" or "dark").

闇 is often used as a noun or のadjective to mean "dark", "darkness" or "the
dark".

暗 is often used as an いadjective to describe something that is dark (暗い).

If you need more imagery to separate them in your head, you could think of 闇
as having more figurative uses like "the dark age" or "an emperor of darkness"
while "暗" might just be talking about a dimly lit room.
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