Nakama means comrade in Japanese, and several shonen manga use this theme.
Example: One Piece, Fairy Tail.
Sure, it might sound nice, but it's not realistic.
Your "friends" don't always save you.
It's just how the world works.

Popular and good examples:
Death Note,Akumetsu, Evangelion(was shonen once).
Kenshin/Embalming have friends but friendship=powers won´t show up.
Durarara!! is about inversions of cliche.
Claymore to a degree.

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Double Arts? Nakama

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You need stronger friends.

Hmm..

Ha...that's straight to the point!

But..it's easier said than done, in my viewpoint.
If you want to know why, I could go on for days.

In the real life, your friends also have their own agenda. Like the well being of their own family and etc etc. So yeah, Shounen teaches a lot of naive things about life.

Maybe, that's why nowadays there are a lot of hikomori. People that used to be the naive idealist nakama power youth, then real life happened, and shatter everything.

OP sounds a bit cynical, but I agre with the above reason. While there are many "fake" friends, there are also friends that simply have different priorities. Not many people are capable of helping you during a sh*t storm, as they have other important priorities and helping usually has far more drawbacks than benefits. Distinguishing between fake friends, normal friends, and close friends has always been a necessary social skill.

What i hate in youth manga is the theme that anything can be resolved or forgiven. Sitcoms for example live on that. A variation is called "liar revealed" but there is always happiness and forgiveness at the end of the rainbow for all. I do like positivity and friendship/devotion can move mountains but not blind or conditionless one. Especially if it writing is hamfisted. Drama writing without consequences is pointless. This blind tolerance is something the Nickelodeon(!!!) Avatar cartoon for example did NOT preach. Even JKR knew that Harry and Draco could never be friend even if an understanding was reached.

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I'm not entirely sure if it's what you want, but these are a few of my favs.
The themes generally revolve around human flaws, so they can get rather dark.
Kuroshitsuji
Full Metal Alchemist
Donten ni Warau

Also worth a mention:
Bokura no Kiseki isn't exactly shonen (it's listed as josei for some reason), but it's a very interesting reincarnation manga (fantasy kingdom - Japanese high school) with an awesome twisting plotline.
One of the main themes of the story is trust and betrayal, as the main characters try to figure out who can be trusted and who is lying.

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Not sure if it counts or not but Black Cat seems to only OCCASIONALLY go it into, it really being important only near the end. With Trains whole, "because you're always alone there's no one there to prop you up when you fall bit," to Creed. And even then when he gets separated from his friends a bit earlier on, rather then then worry about he is all nonchalant because he knows they will be alright. Basically while it is an element of it, it does not feel overplayed to me.

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You're looking for comics aimed at little children/teens and complain about realism? Little strange but ok. You also give two examples and both are action/fighting adventure series. So you want an action/fighting adventure series that doesn't put emphasis on friendship? If you're looking for a shounen adventure/fighting series then you're choices are slim. Sorta like complaining that Pixar gives you happy endings. You know what you're gonna get walking into that sorta stuff.

Also a sorta off topic but the untranslated "nakama" thing came from Kaizoku Fansubs subbing One Piece episodes back in the day. They felt it was necessary for words that have special meanings/were difficult to translate. But that was a really silly decision. Because even in One Piece, "nakama" isn't some glowing, magical word. It's used casually for crew members and new friends alike. Even Viz's translator and some people working with jump believe that it should have been translated.

Even then I'd argue that One Piece doesn't even abuse the friendship trope like you suggest. Despite caring about friends/family in series like OP, HxH, Toriko, Magi, Kingdom (w/e) the main characters still lose.

Maybe in FT or Bleach the friendship will more easily turn one-sided fights, but even then I'd say you're just looking in the wrong place. You'd best be just looking at seinen series instead.

And even then some of them, like Berserk/Claymore/Dorehedoro, will still put strong emphasis on friends/family getting you through hardships. Maybe Vagabond or Vinland Saga? If you're really tired of the "kiddie" stuff then things like Nausicaa or Lone Wolf and Cub or Kurosawa will better suit you.

Or you could skip the fighting requirement instead. Then there are plenty of shounen for you. Most are probably gonna be comedies though, or still contain fighting in some unconventional way.

Noblesse It's getting repetitive & dull lately but I would recommened you to read it for the first three awesome seasons Starting is slow but a good read...

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I think the focus is partly cultural. I think I remember that japan used to have a different system in elementary school where kids were organized into groups and the grades given were given to the group. This was to foster more cohesion in these groups. I think there's a lot more focus on family and ancestors as well. Even in companies, workers are to prioritize the health of the company. Connections between people are a bigger factor in japan, in america it's more of a everyone for themselves kind of thing. I think this is reflected in entertainment, superman, batman etc, usually work alone or with someone of inferior standing. In japanese stuff it's often ensemble. Even in stuff like power rangers people are part of a team.