$\newcommand{\Reals}{\mathbf{R}}$The Cartesian coordinates $x_{1}, \dots, x_{n+1}$, $y_{1}, \dots, y_{n+1}$ are globally-defined smooth functions on the sphere $S^{2n+1}$. As you say, they do not comprise a coordinate system because at each point, one coordinate can be expressed as a smooth function of the others. (Which coordinate is up to you. The only constraint is, if some coordinate is zero at $p$, you cannot solve for that coordinate as a smooth function of the others in a neighborhood of $p$.)
The coordinate differentials $dx_{1}, \dots, dx_{n+1}$, $dy_{1}, \dots, dy_{n+1}$ are therefore smooth $1$-forms. For example, $dx_{k}$ is a smooth $1$-form on $\Reals^{2n+2}$, and by restriction (a.k.a., under pullback by the inclusion map $i$) defines a smooth $1$-form on the sphere $S^{2n+1}$.
Note, incidentally, that while $dx_{k}$ is nowhere vanishing, $i^{*}dx_{k} = 0$ at two points: the standard basis element $e_{k}$ and its negative. That should suffice to convince you that $dx_{k}$ (a $1$-form on $\Reals^{2n+2}$) and $i^{*}dx_{k}$ (a $1$-form on $S^{2n+1}$) are not equal, even though "they're defined by the same formula". The domain matters!
Now, to your questions:
Yes, technically you're letting $i:S^{2n+1} \to \Reals^{2n+2}$ denote the inclusion, and are considering $i^{*}\omega$. The differential of the inclusion satisfies $i_{*}(v) = v$ for every tangent vector to the sphere. That is, if $p \in S^{2n+1}$, then $i_{*}:T_{p}S^{2n+1} \to \Reals_{p}^{2n+2}$ sends each vector $v$ (in the $(2n+1)$-dimensional tangent space $T_{p}S^{2n+1}$) to itself (viewed as an element of $T_{p}\Reals^{2n+2}$).
No, you would not map an arbitrary coordinate to $0$, but instead would express one coordinate as a function of the others and calculate partial derivatives with respect to those coordinates. When you restrict $\omega$, it is locally dependent on only $(2n+1)$ coordinates. Note carefully, however, that doing so forces you to make an inelegant (and unnecessary) choice, only to get the simple answer of the preceding item.
As noted at the top, the Cartesian coordinates define smooth, real-valued functions on the sphere, and their differentials define smooth $1$-forms on the sphere. Consequently, the formula
$$
\omega = \sum_{k=1}^{n+1} (x_{k}\, dy_{k} - y_{k}\, dx_{k})
\tag{1}
$$
defines a smooth $1$-form on the sphere. It simply happens not to a representation in local coordinates on the sphere.
The important point is, if you are given an arbitrary point
$$
p = (p_{1}, \dots, p_{n+1}, q_{1}, \dots, q_{n+1}) \in S^{2n+1}
\tag{2a}
$$
and an arbitrary tangent vector
$$
v = (u_{1}, \dots, u_{n+1}, v_{1}, \dots, v_{n+1}) \in T_{p}S^{2n+1},
\tag{2b}
$$
you can compute
$$
\omega(p)(v) = \sum_{k=1}^{n+1} (p_{k}\, v_{k} - q_{k}\, u_{k}).
$$
The following facts are immaterial:
Not every $(2n+2)$-tuple (2a) represents a point of $S^{2n+1}$;
The $(2n + 2)$ smooth functions in (2a) are not local coordinates on the sphere;
Not every $(2n+2)$-tuple (2b) represents a tangent vector of $S^{2n+1}$.