In topological K-theory, we define functors $K^{-n}$ on the category of compact Hausdorff spaces. With this theory we have the Mayer-Vietoris exact sequence: if $X = A \cup B$, we have an exact sequence $$ \dotsb \to K^{-n}(X) \to K^{-n}(A) \oplus K^{-n}(B) \to K^{-n}(A\cap B) \to K^{-n+1}(X) \to \dotsb.$$ I'm unsure about the details about the subspaces $A$ and $B$ of $X$, however. For since the functors $K^{-n}$ are only defined on the category on compact Hausdorff spaces, I would expect these subspaces to have to be closed. In practise however, I see the Mayer-Vietoris sequence being used with open subspaces, which (in general) are not compact spaces.
I know that the definition of the groups $K(X)$ works for any topological space $X$ (i.e., the Grothendieck completion of the semigroup of vector bundles over $X$). However, since we restrict $K^{-n}$ to compact Hausdorff spaces to ensure that it is a cohomology theory, I'm not sure if it would be right to 'just use the definition' for open subsets of $X$.
I believe we just ask that the interiors of the spaces cover $X$ to apply Mayer-Vietoris which means we can still have a meaningful Mayer-Vietoris theorem even if we ask that the sets are closed.
If you are worried that this stops K-theory from really being a cohomology theory, first you really need to define what a cohomology theory is when we are considering only compact, Hausdorff spaces. Such a thing will always require any subspaces we consider to be compact since how else could we talk about their cohomology?
If what you really don't like is that we aren't defining K-theory in the case of noncompact objects. There is another problem that is even more significant, compact spaces or not. We don't know the positive K-groups! Surely any cohomology theory needs positive groups.
The solution to both is Bott periodicty. It first allows us to define the higher K-groups by taking homotopy classes of maps into the K-theory spectrum, but at this point there is no longer a reason to restrict to compact (or even Hausdorff) spaces. So we've arrived at a fully fledged cohomology theory.