First I must say that mixing JQuery with angular is in most cases a bad idea, So I hope You have a good reason for it. About your question
When importing a file using scripts property of angular.json, You do exactly that - importing the entire file and running it's code. On angular, the will be done prior to the execution of your angular app code.
On the other hand, when importing a module (after installing it using a package manager like npm), You can import only the modules you need, which usually means less code in being executed by the browser. I wrote usually, because when using JQuery you most likely import the entire library in anyway.
I would always prefer installing using a package manager when possible, since:
- It is easier to install and update
- It is a standard when using frameworks like angular
- It allow to import only the actual code I need rather the entire library (Which doesn't matter much in the case on JQuery, but really useful for other libraries).