My reading of your objection is slightly different from anon's, so I thought I'd offer another answer. If I understand correctly, what you are saying is that, while $k=b^2$ would certainly contradict the statement
(1) "$k$ is not a perfect square",
it does not contradict the statement
(2) "$c$ is a positive integer implies that $k$ is not a perfect square"
since $k=b^2$ was derived under the assumption that $c=0$.
My answer to this is that it really is (1) and not (2) that is being assumed in the two proofs you cite. In fact, I'm not even sure where you get the idea that the proofs make the hypothesis that $c$ is a positive integer. It is simply the "other root"; there is no reason why $(c,b)$ must be an element of $S(k)$, or indeed, why $c$ must satisfy any property other than being a root. In fact, $c$ is initially not even assumed to be an integer - otherwise why the need to invoke Vieta's formulas? In both proofs, it eventually ensues that $c$ is a positive integer, and hence that $(c,b)\in S(k)$, but nothing like this is assumed at the outset.
I would add that, if you were correct that the proofs were assuming $c$ to be positive, then there would be no need to prove $c\ne0$ in the first place, since that would already be true by assumption.
Finally, I would point out that defining "natural number" to include both zero and positive integers would not materially alter the overall argument. The aim is to show that the sets $S(k)$ are empty if $k$ is not a perfect square. If $S(k)$ for non-perfect-square $k$ is empty when natural numbers are defined to be positive, it is still empty when they are defined to include zero. The reason is that letting $a$ and/or $b$ equal zero in the expression $\frac{a^2+b^2}{ab+1}$ clearly results in a perfect square. Therefore the extra ordered pairs in which one of both of $a$ and $b$ is zero all lie in $S(k)$ for which $k$ is a perfect square.
I don't know whether enlarging the definition of natural number to include zero would make the proof clearer or more acceptable to you, but if it would, there is no harm in doing so.
Addendum in response to OP's reply: Is something omitted from this text?
So I guess here is why I think that even though clearly if $c=0$ then $k=b^2$ is obviously a square, analogous to the argument with the other proof I've just given, then $(c,b)\not\in S(k)$ doesn't contradict that $k$ such that $ab+1|a^2+b^2$ for $a,b\in\mathbb{N}$ since $c\not\in\mathbb{N}$.
By my reading there should be an additional verb or phrase after "such that" and before
"since". I'll try to give an answer anyway, since I believe that the confusion stems from the belief that there are some top-level assumptions being made about $c$, when in fact there are not. We do impose top-level assumptions on $a$ and $b$. But $c$ is not some object taken from the universe of objects satisfying the same assumptions as $a$ and $b$; it is just a number determined by $a$ and $b$ through a quadratic equation. (In the end it turns out, in the first linked proof, that $c$ satisfies all of the assumptions that $a$ does, except that it is less than $b$. This, however, is a deduction, not an imposed requirement.)
To recapitulate: we aim to show that there are no natural numbers $a$ and $b$ such that $\frac{a^2+b^2}{ab+1}$ is integer but not perfect square. The top-level assumption that the two cited proofs make, seeking a contradiction, is that there are such $a$ and $b$, with $a\ge b$. The value of $k$ is then fixed by $a$ and $b$, just as $k$ is a fixed number in the third proof you offer. Since at this point in the proof, $a$, $b$, and $k$ are just fixed numbers, then we can talk about the properties of the fixed polynomial $x^2-kbx+b^2-k$. In particular, we can talk about its other root $c$, which is also fixed, since it is completely determined by the polynomial. One property of $c$ that we are able to deduce is that it is non-zero, since, if it were zero, that would contradict a known property of the fixed number $k$, namely that it is not a perfect square.
In general I think there can be some unease with proofs by contradiction, especially if you know alternate proofs or have good understanding of the structure of the object under consideration. This unease comes about because you may, before reaching the desired contradiction, encounter statements that don't jibe with the other knowledge you have. You may feel that these statements invalidate the proof. The cure for this to suspend disbelief for the purposes of the proof. You can't allow that other knowledge in if you are trying to reprove the statement from first principles. It is actually completely expected that if, seeking a contradiction, you assume the existence of solutions that turn out to be impossible, you find in the working that these impossible solutions have properties inconsistent with those of solutions that are possible. Operating in suspension-of-disbelief mode, however, those inconsistencies shouldn't be considered manifest until you manage to arrive at a statement plainly in contradiction with assumptions internal to the proof.
Addendum II: While I'm correcting some typos, I'll take one more stab at making this clear. Given numbers $a$ and $b$, the numbers $k$ and $c$ are determined ($k$ by its definition, $c$ by Vieta's formula). If you have made assumptions about $a$ and $b$, you may be able to conclude something about $k$ and $c$. In both the first linked proof and the third proof - the one that you describe in your reply - we assume that $a\ge b$, that $a$ and $b$ are positive (taking anon's correction to the third proof) integers, and that $a$ and $b$ are such that $k$ is an integer. These assumptions imply that $c$ is a non-negative integer.
In the first linked proof, we further assume that $a$ and $b$ are such that $k$ is not a perfect square. From this further assumption it follows that $c\ne 0$. In the third proof, there is a different further assumption, namely that $b$ is positive and minimal. From this different further assumption we conclude that $c=0$. Different additional assumptions lead to different conclusions about the value of $c$.