Bonuses help in keeping trade value for players. Say you want to give a guy 5/50. Could be any number of combinations but, in it's simplest form, a 10m bonus allows you to drop the yearly, evenly distributed, total by 2m per year. Trading an 8m per year guy is easier than trading a 10m per year guy.
For the sake of payroll, there's really no reason to not arb a guy once or twice.