Given an odd prime $p$ and a positive integer $n$, let $QR$ be the set of non-zero quadratic residues in the finite field $\mathbb{F}_{p^n}$. Suppose we have a non-trivial (additive) group homomorphism $f\colon \mathbb{F}_{p^n}^+\to \mathbb{F}_p^+$, where $\mathbb{F}_q^+$ denotes the additive group of the field $\mathbb{F}_q$. Then what can we say about the cardinality of $QR\cap \operatorname{ker}(f)$?
Very limited calculations suggest the answer is always $(p^{n-1}-1)/2$ when $n$ is odd. But things appear to change when $n$ is even. For $p=5$ and $n=2$, the cardinality can be either $0$ or $4$, for example. The odd case seems consistent with this vague understanding I have of the quadratic residues being semi-randomly distributed through half of the field (so of the $p^{n-1}-1$ non-zero elements of the kernel, then it seems reasonable to suspect that half of them would be residues); but I'm not sure how to formally establish this, or see how $n$ being even changes things.
This is an entertaining soup of basic facts about character sums over finite fields. But let me first record the following fact from the comments:
Fact 1. To each element $z\in\Bbb{F}_{p^n}$ we get a homomorphism $f_z$ from the additive group of $\Bbb{F}_{p^n}$ to the additive group of the prime field $\Bbb{F}_p$ from the recipe $$f_z(x)=tr(zx),$$ where $tr$ is the trace map defined by $$tr(x)=x+x^p+x^{p^2}+\cdots+x^{p^{n-1}}=\sum_{\sigma\in Gal(\Bbb{F}_{p^n}/\Bbb{F}_p)}\sigma(x).$$ Furthermore, distinct choices of $z$ yield different homomorphisms, and all the homomorphisms between these groups are of this form.
Proof. This is textbook stuff. The bigger additive group is an $n$-dimensional vector space over the prime field. Hence the homomorphisms are exactly the elements of the dual space, and there are exactly $p^n$ of them. The mapping $f_z$ is a homomorphism of additive groups because it is the sum of such beasts. If $z\neq0$ then the kernel of $f_z$ cannot have more than $p^{n-1}$ elements, because it is given by a polynomial of degree $p^{n-1}$. As $f_z-f_{z'}=f_{z-z'}$ we get as a corollary that $f_z\neq f_{z'}$ whenever $z\neq z'$. Therefore we have listed all the $p^n$ homomorphisms. QED.
I also need to list the following leading actors:
The value of the Gauss' sum is well-known (search for Gauss' sign problem and Hasse-Davenport relation): $$ \begin{aligned} G(p)&=\begin{cases}\sqrt p,&\ \text{if $p\equiv1\pmod4$},\\ i\sqrt p,&\ \text{if $p\equiv-1\pmod4$.}\end{cases}\\ G(p^n)&=-(-G(p))^n. \end{aligned} $$
Fact 2. Let $f_z:\Bbb{F}_{p^n}^+\to\Bbb{F}_p^+$ be the above homomorphism, $z\neq0$. Let $N(z)$ be the number of non-zero squares in the kernel of $f_z$. Then $$2p N(z)=\sum_{a=0}^{p-1}\sum_{y\in\Bbb{F}_{p^n}, y\neq0}e(azy)(1+\eta(y)).$$
Proof. Here $1+\eta(y)=2$ when $y$ a non-zero square, and $1+\eta(y)=0$ otherwise, so this follows from the basic geometric sum. QED.
Next I will concentrate on evaluating that character sum. Let's first fix a value for $a$, and let's include $y=0$ into the summation (so that we can apply the orthogonality of characters).
Let me record that in a sum $\sum_{y\in\Bbb{F}_{p^n}}e(azy)(1+\eta(y))$ the contribution of $y=0$ is always equal to $+1$. Using all of the above in Fact 2, we get the following result:
With the aid of this formula we can explain some of your observations: