With newer versions of AmigaOS, there is an alternative way of launching shell scripts from Workbench, which doesn't involve IconX - instead of an icon of type "Project", one can set icontype to "Tool", tick attribute (protection bit) "script" and add CLI and DONOTPROMPT as tooltypes - that is select "Shell" in the "Start from:" menu and remove the "Prompt for input:" tick. On double click, the script will just be executed.
These tooltypes do not work with WBLoad though, which only report "object is not of required type"...
I would argue that a text file that has S-bit set, by default should rather be treated as a tool than as a project by Workbench (and/or Deficons).
It should also be possible to tick for H and P protection bits from WBInfo.