I believe what you are asking is:
If you have a variable called:
application.data.settings.foo.bar = { some: 'value' }
Is it more performant to access it by using application.data.settings.foo.bar - or to instead say: var bar = application.data.settings.foo.bar and then refer to bar.
My guess is that the assignment to variable is probably slightly more performant - simply because there are less steps for the interpreter to take in order to access the relevant item. If you use application.data.settings.foo.bar - the interpreter has to utilize the reference to the application object, then reference it's data property, then reference its setting property, then reference its foo property, then reference its bar property. This is 5 steps.
If you reference it into a local variable for access - you are still hitting the same object, but you are hitting it directly on each reference.
At the end of the day, however, this is unlikely to be a performance enhancement which is hugely noticeable, unless you are doing a lot of heavy, rapid-access looping or something similar.