I don't have an exact answer for you, but I might be able to offer some decently-related information, as well as a "better-than-nothing" fix.
First, you need a utility called "TDUMT" (I think it's on this website somewhere?). Anyway find it and download it. When you run that program, the button in the middle should say "vehicle manager". Choose that, and scroll through the list of cars and bikes to the Ducati you wanted to edit.
Once you find it, double click, there are sub-tabs lower down in the window that show various things you can edit. Most of it is trivial stuff, but there is a "colors" section for what paints you can select for that vehicle at a paint shop. You can even use the section to view and edit available interior colors for cars.
Unfortunately, this section DOES NOT allow you to easily change if a vehicle can visit the deluxe shop. However, if you had a specific general color or colors in mind, you can use the buttons on the color menu to add new entries from a lot of different named colors in the game's code. (It's not hard to do, but annoyingly none of the buttons have labels, I think once you're on the colors menu and you can see the drop-down box with current paint options, there's a "+" button or "add" or something nearby. Use that to add any colors you want from a large list of names).
That's the "better-than-nothing" fix, but no, it's doesn't exactly allow what you were hoping for.
Documentation for TDUMT is weirdly hard to come by (a lot of guides are either incomplete or poorly translated and way too vague). However, through some messing around I've noticed there is a "Database" option or something on the main screen where you initially clicked "vehicle manager". If the game has any sort of "yes/no" coding about visiting the deluxe paint shop, I'm sure it's in there.
One more bonus note: I once tested adding a light blue color as a purchasable option to the stock game's Ferrari 288 GTO. Interestingly, that vehicle normally cannot visit even the STANDARD paint shop because it only has one color available. Adding a second selectable color through TDUMT allowed that vehicle to visit the standard shop without a problem, because it now had more than one paint available.
Sorry for the long message, hope some of this somehow helps. Good luck!