Sorry about the convoluted sentence structure. Cats and programming do funny things to the way I understand things.
Are you tracking bonuses at the instance level or the global level? If you create a new variable for bonus things, it would make sense for it to have the same scope as the rest of your score related variables. I'm guessing global, but if its a multiplayer game you might be doing something different. So you have a new variable, called BonusRate. It starts at 0. Whenever you get a bonus, you add 0.1 to BonusRate and leave Score alone. Every second, you add BonusRate to score. That way, when you first start off, BonusRate is 0 and nothing happens to the score every second. After you pick up one bonus, BonusRate is now 0.1 and 0.1 gets added to your score every second. After you've picked up two bonuses, your BonusRate is now 0.2, and every second you get 0.2 extra points. If you get a third, it becoms 0.3 etc etc etc
A different approach might be to track the number of bonuses picked up so you can ;display it to the player. Then, if you picked up 5 bonuses, your Bonuses variable is now 5, and every second you do Score = Score + Bonuses*0.1, so every two seconds you get a point.