Hardness of finding roots of a degree $2$ polynomials over $\mathbb{F}_2$ Since every $3$-SAT instance with $n$ variables can be expressed as a  degree-$3$ polynomial over $\mathbb{F}_2$ with $n$ unknowns,  the NP-hardness of $3$-SAT directly translates to NP-hardness of solving(finding roots) $3$-degree polynomials. 

So my question is solving a single degree-$2$ polynomial over $\mathbb{F}_2$ with $n$ unknowns, NP-hard?
It's easy, and in fact I suspect your proof that the "degree-3 version is NP-hard" is flawed somewhere, since the degree-3 version is also easy. Here's the argument for degree-2:

Suppose our constraint is $p(x) = 1$, and assume, since we're only interested in $p$ as a function, that it is reduced mod $x_i^2 = x_i$ (ie that it's multilinear). We can plug in zero, and if it fails to satisfy the constraint, we can conclude that $p$ has no constant term. Next, we try all points of Hamming weight 1. If they all fail to satisfy the constraint, then, since $p$ has no constant term, this means $p$ has no terms of degree 1. [To see this, think of what a Hamming-weight-1 input does to each monomial.] Next we try all points of Hamming weight 2, and, again, if these fail, then, since $p$ has no terms of degree at most 1, this means $p$ has no terms of degree 2. Since $p$ has degree at most 2, the only way these can all fail is if $p$ is the zero polynomial, and of course no solution exists in that case.

This keeps going to higher degrees: (the multilinearization of) $p$ has no terms of degree at most $r$ iff it's zero on all points of Hamming weight at most $r$. So for any constant degree, you get an efficient algorithm.