If your custom code interacts correctly with the page lifecycle, your customizations can execute only when they are needed within the page startup, render, update or exit. The key to making this work is having your code subscribe to the appropriate application event.
If your customizations intend to manipulate the DOM created by CONTENTdm, be warned that approach may conflict with the way the React application needs to use and change the DOM. If the CONTENTdm application cannot find what it expects in the DOM, the app can crash and the end user’s session will be lost. However, if your custom code is creating its own elements and modifying or removing them, there should be no problems on the React side.
If you are used to working with jQuery, note that it relies on a lot of direct DOM manipulation and abstracts some of this manipulation so that it is not always clear when it is happening. It is possible to use jQuery within the CONTENTdm React application but be careful with the scope of those DOM changes. In general, your code should not use jQuery to remove or change elements in the DOM if those elements were created by the CONTENTdm React application. On the other hand, if your jQuery code is creating its own elements and modifying or removing them, it should be safe.
The CONTENTdm website does not use jQuery so it is not already available in the default HTML. If you want to use jQuery in your customizations, your custom code will need to link to it and load it at the appropriate time in the lifecycle. Your website and customizations will likely perform better if you can avoid using jQuery.