Bonus money is usually spread out as well, it's very uncommon for a player to get a huge signing bonus in a single payment - like Haloti Ngata f.e. does this year with the option bonus of $10M coupled with the 1/5 of the $25M signing bonus.

Vilma's last contract had a $6M signing bonus, but that was divided equally to all of the 5 contract years with a $1.2M/year bonus, so players don't usually get the bonus outright - the contract includes $17.2M total of guaranteed money.

Bonuses count toward the overall cap hit, but the difference is that they are usually guaranteed (f.e. signing bonus) and they can be divided in many different ways as opposed to the base salary.

Incentive based bonuses and escalators are a whole other thing.

But I'm not really an expert on the issue.