Note, in the following, when I'm talking about solutions in multiple dimensions compared to ones in one dimension, what I mean is that each coordinate on its own should be considered a single-dimensional solution.
So for instance, if I get $\begin{bmatrix}
x\\
y
\end{bmatrix}
= \begin{bmatrix}
s_1\\
s_2
\end{bmatrix}$, then I consider $s_1$ and $s_2$ two separate solutions, eventhough they normally clearly are only one solution of a two-dimensional problem. This is so I can actually compare with one-dimensional solutions. The whole premise of the question wouldn't make sense if not for that.
The set of algebraic numbers is the set of roots of polynomials of arbitrary degree $n$ with integer coefficients $a_i$.
$$P_n{\left[x\right]} = \sum_{i = 0}^{n}{a_i x^i}\\ \mathbb{\overline{Q}_n} : \left\{ x | P_n{\left[x\right]} = 0 \right\}\\ \mathbb{\overline{Q}} : \text{values of } \mathbb{\overline{Q}_n}\text{ for any } n.$$
If you try plugging in algebraic numbers as coefficients for those polynomials, you won't find anything new. The solutions will all be algebraic numbers as well.
Is this also true if you allow higher-dimensional polynomials?
Say you have a polynomial of the form $a_{2 0} x^2 + a_{0 2} y^2 + a_{1 1} x y + a_{1 0} x + a_{0 1} y + a_{0 0} = 0$ where $a_{i j} \in \mathbb{Z}$ and $a_{2 0}, a_{0 2}, a_{1 1}$ can't all be zero.
If I'm not mistaken, this will not yet suffice since you'll get infinitely many solutions that form a $1$-dimensional subspace. So let's add a second polynomial of the same form to fix a couple points.
$$\begin{align*} a_{2 0} x^2 + a_{0 2} y^2 + a_{1 1} x y + a_{1 0} x + a_{0 1} y + a_{0 0} & = 0 \\ b_{2 0} x^2 + b_{0 2} y^2 + b_{1 1} x y + b_{1 0} x + b_{0 1} y + b_{0 0} & = 0 \\ a_{i j}, b_{i j} & \in \mathbb{Z} \end{align*}$$
and the six highest degree terms can't all be zero, so that at least one polynomial has degree $2$.
As long as these equations are independent, only a discrete finite set of solutions should be left over. I declare these solutions to be two-dimensional algebraic numbers of the second degree. Are these solutions the same as (one-dimensional) algebraic numbers?
By trying out this scheme for the first degree case (so just systems of linear equations), it is easy to see that the results will just be rational numbers which already are fully covered by (one-dimensional) first degree algebraic numbers (i.e. Integers and Rational Numbers). Based on that result, my hunch is that the answer to the title question will be negative: Algebraic numbers already fully cover this case for all degrees and all dimensions. But of course, the degree $1$ case is trivially represented in linear algebra, so it could easily be the case that non-algebraic solutions exist only for higher degrees. So is my hunch correct?
Bonus question 1: (Assuming my hunch is right) Will higher dimensional solutions change in degree? I.e. Can I represent (one-dimensional) algebraic numbers of degree $>n$ as solutions to systems of multidimensional polynomial equations of degree $n$?
Solution counting henceforth will be in the normal sense: $\begin{bmatrix} x\\y\end{bmatrix} = \begin{bmatrix}s_1\\s_2\end{bmatrix}$ is only one solution.
Bonus question 2: Up to how many solutions will a system of polynomial equations of degree $n$ in $d$ dimensions generally have?
You won't get anything new. The points $(x,y)$ that are solutions of your pair of equations have coordinates that are algebraic numbers.
Given two (independent) polynomial equations $f(x,y)=0$ and $g(x,y)=0$ the resultant $R=R(f,g)$ is a polynomial with coefficients in $\overline{\Bbb{Q}}[y]$ with the property that the $y$-coordinate of any point in the intersection is a zero of $R$ (in general the coefficients of $R$ will be in the same field as those of $f$ and $g$). See the Wikipedia page on Resultants for links and more. Of course, when $y$ is algebraic $x$ will be also.
A different way of looking at it is that a point $(x_1,x_2,\ldots,x_n)$ with transcendental coordinates (over the field of definition $K$) will always be a generic point to a variety of dimension that is equal to the transcendence degree of the extension $K(x_1,x_2,\ldots,x_n)/K$. In other words, if you have transcendental coordinates in a solution, then the set of solutions is at least one-dimensional.