The book I am earning from states that the theory of a $\mathcal{V}$-structure, $M$, is the set of all $\mathcal{V}$-sentences that are modeled by $M$. Then it goes on to say that that any theory of a $\mathcal{V}$-structure is complete. So lets look at the structure $NT= (\mathbb{N} | +, \cdot,1)$.
My book says that the axioms of NT are:
$\forall x \lnot(x+1=1)$
$\forall x \forall y (x+1 = y+1 \implies x=y)$
$\forall x \forall y (x+y = y+x)$
$\forall x \forall y (x + (y+1)=(x+y)+1)$
$\forall x \forall y (x \cdot y = y \cdot x)$
$\forall x (x \cdot 1 = x)$
$\forall x \forall y (x \cdot (y+1) = (x \cdot y)+x)$
$\forall^1 S(S(1) \land \forall x(S(x) \implies S(x+1)))\implies \forall x S(x)$
This last axiom is technically a second-order sentence, but I have read that it can be written in a first order language as an axiom schema. So these sentences, by our choice, are in $Th(NT)$. But Godel showed that, only assuming these axioms, there are some true sentences which cannot be derived. So won't these sentences and their negations be missing from $Th(NT)$? I don't understand how my book can claim that $Th(NT)$ is complete.
The line
is extremely misleading. There is an analogue of the second-order induction sentence in first-order logic, consisting of a scheme of axioms as you say. However, this analogue is strictly weaker than second-order induction. This is why your $NT$ can be complete while its first-order version which I'll call "$NT_1$" is not (per Godel): they are not equally strong theories.
In particular, we do have $NT=Th(\mathbb{N}; +,\cdot, 1)$, but $NT_1\subsetneq Th(\mathbb{N}; +,\cdot,1)$.