When I first drew it up, I was thinking in terms of "everybody gets their own bathroom" as though they were motel rooms. For a ship that's mostly in government service, I came to view that as excessive. Maybe two full bathrooms, each shared with an adjoining cabin, one of which also opens to the common area. Senior scout gets one of the two cabins connected to the washroom that doesn't open to the common area.
Oh, well ... if that's where you were going with things, then there is precedent for that sort of interpretation.
LBB S7 has exactly this going on with its deck plans for the Express Tender on p12 in the deck plans backed up by the explanation on p14.
In contrast to that, the Type-J Seeker trades in the 4x 4-ton staterooms for 4x 2-ton cabins instead, so it kind of depends on which way you want to play it with your deck plans.
Of the two, the Express Tender looks like a better deck plan precedent to follow.
One of the issues with a canon Type S is that the interior layout doesn't provide physical separation between the quarters for the crew (pilot, and perhaps gunner) and those for passengers (up to three paying passengers if the ship's being sailed single-handed). This is an invitation to a hijacking -- especially since a one-man crew can't provide 24-hour coverage!
Well ... there's kind of a reason for that.
Type-S Scout/Couriers active in the IISS are basically only going to be carrying "trusted" passengers.
Detatched Duty vessels, awarded as a mustering out benefit, are a different story, of course. Those vessels could be put to "common" passenger service courier/transport duty if the captain wanted to.
As far as "rearranging the staterooms" in concerned on a Type-S floorplan (LBB S7, p17), probably the easily solution to the problem of separating the passenger staterooms from the crew staterooms would be to move staterooms (6 and 7) aft and put the common area forward so as to have a "buffer area" between the forward staterooms of the crew (3 and 4) nearer the bridge and the aft staterooms for the passengers (5 and 6) nearer to the engine room (and aft lounge in 13).
But the simple fact of the matter is that a Scout/Courier is so small (and the crew so small as well) that there almost isn't a good way to "hijack-proof" a Scout/Courier deck plan. There's just too many access points for all areas of the ship. Plus, most ships are operated in a mode where the passengers (if any) are "trusted" because they're being transported under orders by the service, rather than being a mercantile operation open to the public.
My IMTU solution to the problem for the canonical version is that Detached Duty Type S ships are still the property of the Third Imperium
That's OTU.
Detached Duty Scout/Couriers remain the property of the IISS and can be recalled (the ship) to active duty in the event of a declared war.
The only Scout/Couriers that are not subject to being returned to active service in the event of a war are those ships that have been sold as surplus to private interests and entities.
Basically, if you BUY one, it's
yours ... but if you're AWARDED one (as a mustering out benefit), it's still technically
theirs, they're just loaning you the use of it (with a few perks).
This renders them un-saleable in whole or in part, and Imperial law enforcement will be ruthless if you're discovered with stolen Imperial property.
Not true ... they can be sold, as surplus (usually 40 years after construction) ... and there are a LOT of Scout/Couriers that get sold off as surplus. So the "fate" of Scout/Couriers after 40 years of service will vary (quite a lot).
After all, if they couldn't be sold at all, the Type J Seeker wouldn't exist.
In other words, they're mostly hijack-proof in 3I space because there's little profit in doing so.
Except that Scout/Couriers are so ... ubiquitous ... they make excellent cover for infiltration operations by less than savory/honorable types of characters. That whole "best place to hide a tree is in a forest" kind of deal. Most people would never look twice at a Scout/Courier, simply because they're that common ... which then makes them an excellent camouflage for all kinds of nefarious dealings (so long as you don't get caught doing them).
Plus, you're also overlooking the opportunities to use a Scout/Courier in distress as a decoy to lure in a would be rescuer, only to have the rescue crew overpowered in crew on crew combat through the docking hatch between the two ships (yes, Scout/Couriers can play pirate too

).
So in terms of being hijack proof ... I have one word to sum up my thoughts on that notion.
HARDLY. 