I assume that you are bringing this up in the context of an inductive proof, whose inductive step usually starts out with something like
"Assume that $P(k)$ for some number $k$".
Now, the use of 'some' here makes it sound like your (2): $\exists k \in \mathbb {N} : P(k)$
However, this is certainly not the assumption of the inductive step. Consider: suppose we use that assumption. We could then also suppose that $k_0$ is one of those numbers, and maybe we can even show that that means that $k_0 +1$ has property $P$ as well. OK, so what have we then proven? All we would have proven is that there is some number such that it and its successor have property $P$. In logic: we would have shown that $\exists k \in \mathbb {N} : P(k) \land P(k+1)$. Or, discharging the assumption, we obtain $$\exists k \in \mathbb {N} : P(k) \to \exists k \in \mathbb {N} : P(k) \land P(k+1)$$ But that is not what the inductive step tries to show.
The inductive step tries to show that $\forall k \in \mathbb {N} : P(k) \to P(k+1)$. We do that by picking some arbitrary number, assume that it has property $P$, and use that to show that $P(k+1)$.
So here is the difference: instead of assuming $\exists k \in \mathbb {N} : P(k)$, we simply assume $P(k)$ once $k$ has been introduced as an arbitrary number. So, the assumption is really just $P(k)$. Once we obtain $P(k+1)$, we can discharge the assumption and get $P(k) \to P(k+1)$, and by noting that $k$ was an arbitrarily chosen number, we can generalize this for all numbers, and thus obtain $$\forall k \in \mathbb {N} : P(k) \to P(k+1)$$
So, the assumption is really more like your (1), where $k$ is a free variable. Indeed, when the inductive step starts out with:
"Assume that $P(k)$ for some number $k$"
you should really read that as:
"Assume that $P(k)$ for some arbitrary number $k$"
or, better yet, as:
"Let $k$ be some arbitrary number and assume that $P(k)$"
It is $k$ being an arbitrary number (as reflected by it being free) that allows you to conclude with the universal statement that you want.