the I/O Port is used for "De-Fragment" the disks. It is not a mayor problem to do so.
Nor was it back in the days when I had to de-fragment my HDD every few month.
But you still have to do it.
@Henry Link is right that if you from a beginning on know complettly what stuff you want to format your disks for then it is normaly not a problem because it will take some time to fill a 64k Disk.
But lets take sugarcanes for example. I normally have about a 10 stacks of it in my 1k disks before I start building a farm from it.
When I build the Farm I then format a 64k Disk for sugarcane. But until I do not put my 1k disks through a IO Port those initial stacks I had will still take up space in my 1k disks.
Now, it is probabbly not a problem that it is still there because I can make a other 1k Disk or just use the IO Port that is easy as well... But with Refined Storage you have less of a problem with it.
But I think we are now on a level were we are talking about so little time that it not worth considering it as a "disadvantage"
Edit: What I miss with AE2 is a way to Void stuff once a formated Disk is full. I would have to setup a storage Bus that has its priority set between the disk Drive and the normal drives and pointing to a trashcan...
But this leads to maintain 2 filters in the Storage Bus. If I forget one I will our fill my system or send everything to trash that I wanted to store.