Bonus Points Mechanic

It's hard to suggest anything thematic without knowing the theme, but cards definitely work better as a hidden point mechanic than say a hidden track (open to cheating) or collecting dice to be rolled at the end (too much randomness).

One way to tie the theme to the mechanic is to have distinct decks of hidden-point cards for each reason one might get a bonus. There could even be some public points for getting certain combinations of hidden cards. For example, a certain warlike faction might get one public point every time he or she collects three different combat-related cards while a more cosmopolitan faction gets one public point every time he or she collects one of each of the three card types.

The hidden face of the card could give a certain number of points, or some variable (but unambiguous) number of points based on the board state at the time cards are revealed. For example, "3 points if this player controls the SWAMP OF SORROWS region, otherwise 1 point".

One option is to force players to reveal all cards at the end, or allow them to reveal at most one card per turn if they think the conditions are likely to get worse. The revealed card would move the public score and have no further power to chance anything. Whether such a revealed card still counts toward collecting sets is a separate decision.

Hope that made sense :-)

Five tribes - has the market in which players collect up to nine different commodities with an increasing value for each one. (Well I guess this is technically public info if you have an amazing memory.)

Jamaica has an interesting cards and an card circulation mechanic.

T'zolkien has worship tracks and depending where you are on these you get rewarded or punished at certain points during the game.