First, the answer to Question 2 is YES and it is not hard to show. For $q=\frac{a}{b}$, by assumption $(a,b)=R$. In particular,  $1$ is generated by $a$ and $b$ so we have $1=ax+by$ for some $x,y\in R$. Take $n$-th power on both sides we see that $1$ is generated by $a^k$ and $b$. Therefore $(a^k,b)=R$ for any positive integer $k$. 

For any $f\in\mathrm{ker}(\mathrm{eval}_q)$ where $q=\frac{a}{b}$ we have $f(X)=(X-\frac{a}{b})g(X)$ where $g(X)\in K[X]$. Write $g(X)=\sum_{i=0}^{n}a_i X^i$ where $a_i\in K$. Since $f(X)\in R[X]$, by induction we see that $a^{i+1}a_i\in (b)$ for all $i\in\{0,1,\cdots,n\}$. We also have $a_n\in R$ as the leading coefficient of $f(X)$, which implies that $a_n=a_n(a^{n+1}x+by)=a^{n+1}a_nx+b a_n y\in (b)$ for some $x,y\in R$ since $(a^{n+1},b)=R.$ Now we have $a_{n-1}\in R$ since the coefficient of $X^n$ in $f(X)$ is in $R$ and that $a_n\in (b)$. Together with $a^n a_{n-1}\in(b)$ and $(a^n,b)=R$ we conclude that $a_{n-1}\in (b)$. Repeating this process, we see that $a_i\in(b)$ for all $i\in\{0,1,\cdots,n\}$. Therefore $f(X)\in (bX-a)$.

Second, it is true (as shown by proof of 3.) that if $R$ is GCD, then under the assumption that $gcd(a,b)=1$ (i.e. weak version of being coprime), we also have $\mathrm{ker}(\mathrm{eval}_q)=(bX-a)$. However one cannot simply argue which special case is $``stronger''$: on the one hand, confirmation of Question 2 requires only property of the element $q$ while Point 3. requires GCD property of the whole ring $R$; on the other hand, Point 3. does not require any extra property of the element $q$ since for a GCD domain, any element in the fractional field can be written as $\frac{a}{b}$ where $a,b$ are weakly coprime. But if we only assume that the single element $q$ can be written as $\frac{a}{b}$ where $a,b$ are weakly coprime, the conclusion no more holds and a typical example for the failure is as stated in the next paragraph.

Third, a very rough answer to Question 1 is NOT REALLY- and NO to the ``In particular'' part: For example, consider a number ring case where $R=\mathbb{Z}[\sqrt{5}]$ and $q=\frac{\sqrt{5}+1}{2}$. Then one can see that $\mathrm{ker}(\mathrm{eval}_q)=(2X-(\sqrt{5}+1),(\sqrt{5}-1)X-2, X^2-X-1)$ which is not principal any more. We know that $R$ is not integrally closed, let alone GCD.