Suppose $X$ is a scheme of finite type over $\mathbb Z$. I want to prove that:
(1) The residue fields of closed points of $X$ are finite;
(2) For a given $q=p^n$ with $p$ prime, there is only a finite number of closed points of $X$ whose residue field is $\mathbb F_q$.
For (1), I see that one has to use some form of Nullstellensatz. First, we suppose $X=\operatorname{Spec}(A)$ affine, and $A=\mathbb{Z}[X_1,...,X_n]/I$. We need to show that if $m$ a maximal ideal of $A$, then $A/m$ is finite. Note $p=\mathbb Z\cap m$. If $p$ is maximal, we get that $A/m$ is of finite type over $\mathbb F_p$ thus a finite extension by Nullstellensatz and we are done. But $p$ could be the $(0)$ ideal in which case I neither conclude nor get a contradiction.
For (2), we can again argue locally, so we need to show that $A$ contains only a finite number of maximal ideals $m$ with $A/m$ of fixed cardinality $q=p^n$. I get an impression that to count these ideals its the same as to count the number of automorphisms of $\mathbb{F}_{q}$ which fix $\mathbb F_p$, but the corrspondence is not bijective, so we only get an upper bound which is enough. Is this idea correct?
In (1), the assertion that $\mathbb{Z}\cap m$ cannot be $0$ follows from the version of the Nullstellensatz which applies to arbitrary Jacobson rings (rings in which every prime is the intersection of the maximal ideals containing it), rather than just fields. This general Nullstellensatz says that if $R$ is a Jacobson ring and $A$ is a finitely-generated $R$-algebra, then $A$ is Jacobson and for any maximal ideal $m\subset A$, $m\cap R$ is maximal in $R$ and $A/m$ is a finite extension of $R/(m\cap R)$. Applying this with $R=\mathbb{Z}$ immediately gives that $\mathbb{Z}\cap m$ cannot be $0$ in your case.
Alternatively, you can deduce that $\mathbb{Z}\cap m\neq 0$ from just the Nullstellensatz for fields and the Artin-Tate lemma as follows. If $\mathbb{Z}\cap m=0$, then $A/m$ is a finitely generated $\mathbb{Q}$-algebra and hence is a finite extension of $\mathbb{Q}$ by the Nullstellensatz for $\mathbb{Q}$. By the Artin-Tate lemma applied to $\mathbb{Z}\subset\mathbb{Q}\subseteq A/m$, the fact that $A/m$ is a finitely generated $\mathbb{Z}$-algebra then implies that $\mathbb{Q}$ is also a finitely generated $\mathbb{Z}$-algebra. This is clearly false (any finitely generated subring of $\mathbb{Q}$ can have only finitely many different primes appearing in denominators).