Yes half of it is hard to reach bonuses, however, it all goes against the cap. The reason for that is because they are performance bonuses you won't know until after game 82 whether or not he has reached them. As such, say there is a bonus for 30 goals, he could enter game 82 with 5 goals and still technically have a chance at 30. (although wholly unrealistic) So all rookie bonuses go against the cap.
Whereas with Mathieu Schneider, his were based off games played which you can judge part way through the season, so the cap application is different.