Symplectic case: Here are two reasons (not necessarily the only ones) why $\operatorname{GSp}_{2n}$ is more convenient to work with than $\operatorname{Sp}_{2n}$.
Firstly: there is no Shimura datum with underlying group $\operatorname{Sp}_{2n}$; you need the "extra room" provided by $\operatorname{GSp}_{2n}$. In practice, this means that although you can define Siegel Shimura varieties as varieties over $\overline{\mathbb{Q}}$ working purely with $\operatorname{Sp}$, there is no sensible way of describing canonical models over number fields until you bring in the larger group
Secondly: The general symplectic group has a richer theory of Hecke operators, because you can consider the action of matrices like $\operatorname{diag}(1, ..., 1, p, ..., p)$, which normalise $\operatorname{Sp}_{2n}$ but aren't contained in it. Having this larger Hecke algebra means that, although strong multiplicity one doesn't hold for either group (except for $n = 1$), it is "closer to being true" for $\operatorname{GSp}$ than $\operatorname{Sp}$ (i.e. the $L$-packets are smaller).
Unitary case: Here the issue is a bit more nuanced because there are various ways of choosing the Shimura datum: roughly, you can choose a Shimura datum for $U(a, b)$ which looks like $z \mapsto \operatorname{diag}(z / \bar{z}, \dots, z / \bar{z}, 1, \dots, 1)$, or you can choose one for $\operatorname{GU}(a, b)$ which looks like $\operatorname{diag}(z, \dots, z, \bar{z}, \dots, \bar{z})$. Each of these has its merits for different things: working with $\operatorname{GU}(a, b)$ gives you a nicer moduli-space interpretation for your Shimura variety (it is of PEL type), so its canonical models are easier to describe; but it is the $U(a, b)$ one which has the nicer Hecke theory.
I have the impression that there is a shift under way in the recent literature. 10 years ago, most of the arithmetic theory of automorphic forms on unitary groups (Shimura varities, Galois representations etc) was developed using $GU(a, b)$, as in the Skinner-Urban paper, or the Harris–Taylor book on local Langlands. However, more recently, people seem to have got better at working with non-PEL Shimura data; thus the recent work on unitary special cycles (arithmetic Gan–Gross–Prasad conjectures, etc) is mostly being done in the context of actual unitary groups. This paper of Rapoport–Smithling–Zhang and this paper of Jetchev have some useful discussion of the relations between the $U$ and $GU$ Shimura varieties.