I would suggest that, yes it's good practice to comment on code that has been removed but not in the code itself.
To further clarify this position, you should be using a source code control system (SCCS) that allows some form of check-in comment. That is where you should place the comments about why code was removed. The SCCS will provide the full contextual history of what has happened to the code, including what has been removed. By adding check-in comments you further clarify that history.
Adding comments in the code directly simply leads to clutter.