"However" is basically intended to be introduced as a parenthetical comment.
The problem is that it it is placed in a spot where it looks ambiguously like a conjunction.
There is considerable flexibility in the language. For instance, suppose instead of "however" we introduce the a phrase like "you know" or "come to think of it", or "I suspect":
Although some of the plots are transcendental, the justice deeply rooted in people's mind, I suspect, will surely applaud for the victory of him.
Although some of the plots are transcendental, the justice deeply rooted in people's mind will, I suspect, surely applaud for the victory of him.
I suspect, although some of the plots are transcendental, the justice deeply rooted in people's mind will surely applaud for the victory of him.
Although some of the plots are transcendental, the justice deeply rooted in people's mind will surely applaud for the victory of him, I suspect.
Basically "however" is acting as a comment phrase of this type and not as a formal conjunction. It is acceptable because it reinforces the "although", or at least does not outright conflict with it semantically. "However" can be put in all those same places as "I suspect", and just makes a comment that the second clause is in spite of the first clause.
But, as I will get to in a moment, there is a reason why we perceive a slight problem specifically with the sentence.
Basically both of these forms can mean "S2 in spite of S1":
Although S1, S2.
S1; however, S2.
so there is synergy between "although" and "however".
What is going on in the first example is that the "although" relativizes the clause. S1 is a subordinate clause of the main clause S2, creating a big clause.
Now consider this pattern:
However, although S1, S2.
In this pattern, built on the first example, S1 and S2 are still relativized, and so the "however" applies to both of them as a unit, and has a relationship in particular with S2 which is the main clause to which S1 is subordinated.
There must be some earlier clause S0 which is being contrasted by "however", that is:
S0. However, although S1, S2.
Now the meaning is something like: "in spite of or in contrast with S0, and in spite of S1, we have S2".
Anyway, since we can have an introductory "however" in front of the whole clause which isn't functioning as a conjunction with the earlier S0, it is also legitimate that we can move it around within the clause, like we can do with any other introduction such as "in my opinion", "I suspect", "surprisingly", "unfortunately". For instance, we can move it way into the middle of S2:
S0. Although S1, S2a, however, S2b.
Concrete example:
Jack gets top grades without studying hard. Although Janet studies hard, she, however, maintains only a C average. [Janet gets only C's, in spite of studying hard, which is in contrast to Jack]
And now, finally, we get to the crux of the issue. Suppose the above "however" moves into this position:
S0. Although S1; however, S2.*
Oops! There is a problem, because it now resembles the conjunctive "however" which relates S1 and S2, not S0 and S2, as in:
S1; however, S2.
Concretely:
Jack gets top grades without studying hard. Although Janet studies hard; however, she maintains only a C average.*
If we write the "however" in the conjunctive style semicolon-however-comma it really jumps out as wrong. If we just put commas, it is acceptable because we are able to understand it as the commentary "however" linking back to the first sentence:
Jack gets top grades without studying hard. Although Janet studies hard, however, she maintains only a C average.
In other words, we can use this in speech, but when we write it down, we must not use semicolon-however-comma, and for best clarity, we should probably avoid it, at least in writing, by moving the "however" elsewhere:
Jack gets top grades without studying hard. However, although Janet studies hard, she maintains only a C average.
Jack gets top grades without studying hard. Although Janet studies hard, she maintains only a C average, however.
Etc.
It doesn't sound natural at all. Even if you wrote:
*Although he's got a good job now, yet he complains.
which would be a more natural place for yet.
The use of though and yet seem to be redundant here, and I would only use one or the other:
He's got a good job now, yet he complains.
Although he's got a good job now, he complains.
He complains although he's got a good job now.
But here I was using yet as a conjunction.
If you want to use it as an adverb - which introduces a reference to time - then Damkerng's answer is the right one.
Although he's got a good job now, he hasn't complained yet.
This last sentence is grammatically correct but its meaning is illogical, it is difficult to imagine someone who has a good job complaining.
Best Answer
I don't think they are redundant and the (very common) structure does add a bit of meaning in this case. Here's my analysis:
Yet emphasizes surprise or irony in compare/contrast. Nevertheless is an adverb meaning "in spite of that" and applies to the relationship between "little time" and "develop". Here is the original and my "interpreted" sentence to show how I understand the distinctions (roughly):
ORIGINAL: Running an insurance agency left Charles Ives little time for composition, yet he nevertheless developed a unique musical idiom.
INTERPRETED: Running an insurance agency left Charles Ives little time for composition, but surprisingly he developed (in spite of "little time") a unique musical idiom.
Sorry it's a little awkward to use a parenthetical expression, but its the best way I could explain this concisely. Compare with a sentence in which nevertheless would not work out so well:
"The visitors complained loudly about the heat, yet they continued to play golf every day." (From Guide to Grammar and Writing.)
"The visitors complained loudly about the heat, yet they nevertheless continued to play golf every day."
In the second sentence, I think nevertheless is too wordy. It's also vague: is nevertheless compared to their complaining, or to the heat, or to both?