In addition to definite sightings on S-28, -37 & -41, now we see The Trunk clearly on yet another boat:
And it revises the plausibility that S-38, earlier rejected (based on a questionably annotated pic) may indeed have been a Trunk-bearer after all - particularly since both her closest-sisters - S-37 and (now) -39 - were packing trunks while stationed right alongside her, in the Philippines. (Though I still think the pic in question was taken in 1938, not '28.)
So we now have definitely four - very likely five - boats with The Trunk, fully (at least) 75% of them stationed together in the Philippines, at the outbreak of the war. This is very much per Donny's hypothesis - with the notable exception that the Far East commando/resupply functions must have been anticipated significantly before the outbreak of (open) hostilities.
In any case, if anybody out there knows of any other pic(s) showing The Trunk - especially on any additional boats - do let me know!