One issue is that very often the "magic" happens in imported modules, so you can't really see what is happening unless you drop down to a text editor anyway. Then there is the infamous issue of modules not automatically reloading even when rerunning the Notebook.

That in theory shouldn't be too bad. Though, there have been some things like %sql I remember using in one notebook, which was essentially a macro for making a datatable from a SQL expression, but it wasn't something you could just copy directly.