I don't know why they were removed but I can imagine there is a serious performance impact if they are left there, especially for applications with tens of millions of rows in the audittrail object. From what I understand they're also not really needed for the functionality of the module.
Those fields where intentionally removed because of the overhead (as Bas indicates).
Most of the time those fields are not necessary, if you really need it you can always add those fields back.
For your information, those fields have been removed in the version where a new option for auditing has been added. Having those system fields and not using them can slow down your app for no good reason.
Another thing in the Audit trail module that slows your application down is having all entities inherit from the same superclass entity. That is a slow process that isn't really necessary.
See the documentation on how to improve this:
Below is the part of the documentation on how to improve your performance on entities that you want to audit. This is especially relevant if the entities are changed quit often.
Association & events (you should use this option)
Inheritance: (avoid this option)
Bas - New answer because my response was too long.
Thanks for the response. I can imagine performance impact too - however, the entity I was asking about was the one that is used as the generalization for objects where you want to track changes. The actual log and logline entities where change information is stored track all of the system attributes, so I guess the performance impacts have been anticipated during development.
Mike