It's sort of like with Bob Odenkirk: there's something pliable and raffish about Odenkirk's face, which is partly why he's well-suited to this particular character. It's acting, of course, but there's also something about that face -- those arched, vaguely sinister brows hanging over beady eyes that so easily alternate between harried, doleful, and conspiratorial. Plus, there's the droopy,
cartoonish elasticity of his mouth, which seems tailor-made not only for flashing charmingly disreputable smiles, but also the most despondent grimaces (at Jimmy's most wretched points, it seems like Odenkirk's chin is trying to disappear into his bottom lip). In the same vein, a lot of people talk about the strange spectacle of Cranston's wrinkly mien or the world-weariness that seems indelibly etched onto Jonathan Banks' face.
Anyway, back to Nacho: as I was saying, Mando's voice is one of the ways in which he's set apart from a more stereotypical brand of gangsterism and machismo. If Odenkirk's physicality suggests something other than the world of competent, professional lawyers (a world that Jimmy covets), then little details like Nacho's voice, incidental as they may be, signal something similar: his vaguely ill-fitting place among the upper echelon of a criminal empire, perhaps? In other words, the serendipitious fact of Mando's soft-spoken voice may provide a way into talking about this character and his significance, even at this early point. It's a small performative detail that speaks to a larger possibility: Nacho doesn't perfectly cohere with the established criminal mold (if Gus were his boss, this would be a different discussion, but Tuco is defining top-tier criminality in this context; besides, like I said earlier, Nacho isn't quite like Gus, either, which further suggests his incompatibility with upper-echelon crime).
Also, I think I read somewhere that Nacho even resents the fact that he's called Nacho (it's something of an imposed nickname and perhaps he feels that it infantilizes him or is vaguely mocking). Later on, in
Breaking Bad, Saul will refer to Nacho by his full, and probably preferred, name: Ignacio. Details like these suggests a character that wants to ascend his second tier position but can't due to imposed judgments and intractable circumstances. This has a lot to do with the fixed hierarchy of Tuco's business, but perhaps also relates to how, like Jimmy, Nacho has come to be characterized and reduced by those around him.
It suggests a theme of how we can come to be defined, against our personal will and aspirations, by a mixture of biological happenstance and social judgment (among other things). Remember, both Nacho and the Kettlemans, among others, quickly defined Jimmy based on some very early and paltry impressions. Jimmy's vibes and his bearing were apparently strong indications of his character. These precipitate (but perhaps not entirely inaccurate) judgments constitute a battle of attrition against Jimmy's soul: the more he's told that he seems like a bad guy, the more likely he is to capitulate to this external characterization of himself. That's why this latest judgment (in "Pimento"), which is not precipitate but has actually been percolating for years, and comes not from strangers but from family, is so devastating. I'm not of the belief that everyone is helpless against such things, but I appreciate the fact that the show is examining the considerable struggle of trying to control our destiny in the face of these kinds of external obstacles and judgments.
So, yeah, maybe Nacho is a guy who similarly has to deal with having his agency curtailed by the perceptions of others (not simply because of his voice, of course; what I'm saying is that this little performative detail fits into the theme of being unfairly pigeonholed/externally determined, and vaguely signals the idea of Nacho's difference and how this might relate to his impeded ambition, undermined place in the criminal world, etc.). Jimmy isn't seen as a bona fide lawyer, so he isn't allowed to become one, and Nacho probably isn't seen as a guy who could pass muster as a criminal kingpin (at least if we consider that, in Nacho's social circle, Tuco is Chuck, and therefore represents the unobtainable professional gold standard -- incidentally, like Chuck, Tuco is also struggling with his own psychic troubles and seems insecure about his status).
Perhaps, then, we can understand Nacho as another ambitious careerist whose dreams are both informed and prohibited by "familial" bonds. As Mike indicated, Tuco isn't the type who would brook Nacho's moonlighting -- the Kettleman scheme, the pills, etc. -- which is why secrecy is needed. Jimmy gets the mailroom, and Nacho gets to play second fiddle in a crime empire. They're both denied upward mobility by those in power, and they're not happy about it. The basis for this denial is complicated, but the show, subtextually and textually, is suggesting that this is partly related to maddeningly involuntary factors: not quite fitting the part, so to speak.
Some of these interpretations are speculative and tentative in nature, but my argument is partly based on how I've noticed Mando describing his character (he's referred to Nacho's "love" for Tuco, and something about how Nacho has his eyes on something bigger than his current lot; the latter, at least, has been made pretty obvious in the show itself).