I have created a lot of crop presets over the years and went to clean them up today as my new Windows machine has a different resolution so I need to recreate many of them. I came here to ask how to do exactly that. Thing is, when I decided to add a screenshot to this post I tried once again to overwrite an existing preset with a new one, something I knew I wasn’t allowed to do. This time time around I read the entire error message and discovered the hidden trick. 
For the next person looking to delete their crop preset (likely my future self! 
), simply hold the Option key when selecting the Preset from the list. Doing so will result in Acorn confirming you’d like to delete it.
I was tempted to say there’s gotta be a better way of exposing this functionality but after looking at the inspector layout for a while I came to appreciate the approach you choose. 
++dave;