So following up from #traitgate, there seems like a lot of the "missing" traits are actually traits that have been removed, changed or added during the last few years. The database have not been updated. This is the case for ALL cards, not only special cards and SBC cards. I'll add more as I discover them
Traits that don't exist anymore, or are hidden
"Dives Into Tackles"
"One Club Player"
"Tries To Beat Defensive Line"
Traits that have a different name in game (database showing old names
"Sweeper Keeper" replaced with "Rushes Out Of Goal"
"Ultimate Professional" replaced with "Team Player"
"Corner Specialist" replaced with "Set Piece Specialist"
There are both "Chip Shot" and "Shooting - Chip Shot" in the database. "Chip Shot" in the database means "Outside Foot Shot", while "Shooting - Chip Shot" shows up as just "Chip Shot" in game.
"Takes Powerful Driven Free Kicks" shows up as "Power Free-Kick" in game.
Traits that are not in the database, but show up in game
"Saves With Feet"
"Comes For Crosses"
So this might be the reason that your Prime Henry doesn't have "Tries To Beat Defensive Line" and Prime Rui Costa doesn't have "Playmaker" - they don't exist anymore.