As it happens, this very point was the subject of a discussion John Baez and I had here. (Part of a long discussion on the $\omega$'s of models of ZF.) John's viewpoint is that "standardness" is a relative concept.
This question cannot be totally disentangled from philosophical issues (but there are some purely mathematical aspects, which I'll address below). If you're a strong Platonist (like Gödel), you believe there is a unique mathematical universe of sets "out there". Call it $V$; then by definition the standard $\omega$ is the $\omega$ of this $V$.
If you prefer to hedge your bets, but still take a more-or-less realist stand, then you might like what we called the "three-decker sandwich". There is some universe $V$, the "outermost" universe; standardness is relative to this. We make no ontological claims about $V$; maybe there are a variety of "universes" that could serve for $V$. Inside $V$ is a model $U$ of ZF, and $\omega^U$ is standard if it's isomorphic to $\omega^V$. The locution "the standard $\omega$" is rejected as unnecessary, and burdened with metaphysical assumptions.
Of course, if everything is developed relative to $V$, then it fades into the background. It's needed mainly to give meaning to the term "standard". (Also in locutions like "the standard $\in$".) The "three-decker sandwich" is $\omega^U\subset U\subseteq V$.
The three-decker sandwich helps explain how non-standard $\omega$'s "work". Consider $\omega^U$. We have $\omega^V\subset\omega^U$, indeed it's a proper initial segment. At the bottom of p.44, Halmos defines $\omega$ as the intersection of all the "successor sets" (aka inductive sets) contained in a set $A$. Now, $\omega^V$ is a successor set, but it does not belong to $U$. That's why $\omega^V$ is smaller than $\omega^U$, even though $V$ is larger than $U$. Informally, the "inhabitants" of $U$ cannot "see" $\omega^V$, and so they compute the intersection incorrectly.
What about the idea that $\omega$ consists of the elements that can be obtained by starting with $\varnothing$ and applying the successor function $n$ times, with $n\in$ "the standard model $\mathbb{N}$" of the Peano Axioms with 2nd-order induction? Halmos does not have a formal theorem expressing this. Rather, he says that $\omega$ provides a rigorous counterpart of the intuitive description that the natural numbers are 0,1,2,3, "and so on". Then in the next chapter, he shows that $\omega$ satisfies the 2nd-order Peano axioms. In a set-theory context, $\mathbb{N}$ is essentially defined to be $\omega$. The two notations emphasize different aspects of the set of natural numbers: $\omega$ as an ordinal, $\mathbb{N}$ as a free-standing structure, whose signature (in the sense of mathematical logic) would include + and $\cdot$ but not $\in$.
Back to philosophy. If you're some breed of formalist, then the universe of all sets is a fiction. All that matters is what you can prove in some formal system like ZF. In ZF, one can give a formula $\varphi(x)$ and prove that there is a unique set $w$ satisfying $\varphi(w)$; moreover, $\varphi(x)$ is a formalization of the usual definition for $\omega$. Statements mentioning "the standard $\omega$" are rephrased using $\varphi$.
No doubt there are many other philosophical positions one might take. Perhaps one accepts the "multiverse of universes" (like Joel David Hamkins), but feels all the “legitimate” ones have the same $\omega$. (This seems to be the view of Scott Aaronson.) The argument for this: our intuitions about the natural numbers seem much more concrete and solid than about the entire universe of all sets, which disappears into the misty heights with the higher cardinals. (And is fuzzy around the edges, thanks to things like the Continuum Problem.) Others might feel that there's plenty we don't know about $\mathbb{N}$; maybe the notion of "the standard natural numbers" is a bit foggy after all.
As for the textbooks, these usually keep philosophy to a mininum. A couple of quotes from Halmos' preface:
The purpose of the book is to tell the beginning students of advanced mathematics the basic set-theoretic facts of life, and to do so with the minimum of philosophical discourse and logical formalism.
A more important way in which the naive point of view predominates is that set theory is regarded as a body of facts, of which the axioms are a brief and convenient summary...
I don't know what Halmos' personal philosophy was, but these quotes suggest a stylistic Platonism. As long as we're working in some fixed "outermost" set-theory universe $V$, we're entitled to use the notion of "the standard $\omega$". Pedagogically this is fine: it seems to have a clear intuitive meaning, and if we're not discussing non-standard models, might as well let sleeping dogs lie.
An analogy. Quantum mechanics boasts a large body of controversy over its proper interpretation. David Mermin once noted that most physicists in practice go by the "shut up and calculate" interpretation. With regard to these set-theory matters, I dare say most mathematicians are happy with "shut up and prove theorems" most of the time.