well those warnings are usually implemented for a reason.
I don't have any experience with projects exceeding a certain amount of pages, but I do know of cases where stuff like the recommended maximum of layers was ignored which led to corrupt data which was pretty much useless.
Usually there are a lot of ways to save unrequired elements, if you like
you can let me know your project details (ProjectID, installation etc.) and I'll give it a quick look to check what could be optimized.