This will create a problem if the same package gets loaded both automatically and manually, with conflicting options. However, you will also have a problem if you do not, and the package later changes so as not to include the other automatically.
In many cases, a package that includes another will be able to pass options through to it. For example, \usepackage[leqno]{mathtools} passes the leqno option to amsmath. You should use that interface if available. If there’s a special option to load a package from another class or package, such as hyperref has for several other packages, there’s probably a reason for that.
Otherwise, if you need particular options for the class another is built on top of, your best bet is to load the base package yourself first. Usually, the second package will not load it again.
If the base package has a command to switch on options after it’s loaded, a well-written package that needs that option set should use that command, and you can do the same. This ought to avoid clashes from loading the package twice with different options.
If you don’t care about the options to the base package, I usually, but not always, still include it. Consider whether it’s a stable part of the interface that one package is built on top of the other or an implementation detail that might change.
For example, mathtools is designed to extend amsmath and unicode-math is designed to extend fontspec, so I would include only the top-level package. On the other hand, if a publisher’s class or stylesheet included a font package, or twocolumn, I’d figure that’s liable to change if the paper is ever reprinted.
\inputexecuted by\usepackageassure that the package is loaded only once. – Phelype Oleinik Aug 15 '18 at 15:16\usepackageand notloadpackage, right? – moewe Aug 16 '18 at 07:22mathtoolsalways loadsamsmath, so if I use the former I do not load the latter.amssymbloadsamsfonts, I normally loadamssymband then do not loadamsfontsexplicitly. So I guess if it is an established and integral part of package X to load another package Y and I'm unlikely to ever use Y alone I do not load Y explicitly. – moewe Aug 16 '18 at 07:29