AE shape VS Illustrator file

They will simply render at the same speed as far as you, the user are concerned. We are talking nanosecond differences here, if at all. That kind of is the point: Whatever issues you have are influenced by other factors like the complexity of the artwork, specific features being used, keyframe timing, blend operations with other layers or whatever and unless we know what's going on, we can't tell you how to fix or improve it.

Mylenium

This entirely depends on the contents and what the template needs to do. You need to be much more specific before anyone can advise on whether this would bring any performance gains plus of course the usual of providing system info, effects used and so on. A single effect could be causing this totally unrelated to the layer type and then of course rebuilding the project would not achieve anything.

Mylenium