I think you're missing the point. If you don't have a tickbox you've just made every single destroyer in the game which doesn't have a cargo set for at least one subsystem scannable.
I might be missing something indeed, because it still doesn't make sense to me.

What does it matter if they're all scannable, if there is nothing to scan and thus scanning won't happen?
This is the way I see the current behaviour:
1. You can only scan subsystems which have cargo.
2. You can only put cargo on a subsystem if you toggle "toggle subsystem scanning" on, and it's off by default.
...which already assumes that if you put cargo somewhere, you want it to be scannable, so I have difficulty seeing how the "toggle subsystem scanning" checkbox isn't just an unnecessary extra hoop to jump through. If I need to make cargo scannable before I can put cargo anywhere, then the presence of cargo should be the only cue the game needs from me. As it is I feel like I need to tell FRED that "hey, I'd like to have subsystem cargo, so could you please make subsystem cargo scannable so I can put in the subsystem cargo".
Unless, as I said, I am still missing something.
In addition you've complicated the code for scanning as now the code has to decide if a ship is scannable on parse by checking if there are any cargoes set for any of it's subsystems.
Now if you want to suggest moving the toggle button to the initial status editor (IIRC it's on the ship flags editor) that's a completely different matter.
Well, sure, the more reasonable behaviour being technically more difficult to implement (or having no one willing to do it) is of course an understandable reason not to do it.
Anyway, yeah, the checkbox would make more sense in the initial status editor, I think.
And I guess I could volunteer to write a patch for determining scannability at parse time as per my suggestion,
if it so happens that I'm not missing something important and it'd actually be an acceptable change. It sounds like it can't really complicate the code much, but that's certainly an assessment I don't want to try to make before taking a look.