Certainly, with web applications you would want the least amount of latency possible. This is a normal UX scenario -- as you indicated, there are factors which can simply be out of the hands of the application such as network connectivity.
In cases like that, indicating to the user that something is happening makes for a better experience than not doing anything, or in the worst case (which certainly shouldn't happen these days) blocking the user's browser.
In cases like that, indicating to the user that something is happening makes for a better experience than not doing anything, or in the worst case (which certainly shouldn't happen these days) blocking the user's browser.