I was reading something this weekend that said rating 1-3 would be pocket-sized while rating 4-6 would be briefcase-sized. Naturally, now that I need a page reference, I cannot remember where I read it.
I actually like the optional rule from Bullets & Bandages, lest every single runner show up with a rating 6 medkit tucked under their arm, but I also know it's not Missions-legal.
Ignoring B&B for the moment, I might go with 12" x 18" x 4" for a rating 6 medkit. Your pistol case (12x9x5) would be good for a rating 4 medkit at my table.
Edit: Nevermind, I was mis-remembering the "handheld case" line from the core rulebook. I thought it said briefcase.