I actually think bonuses and equity grants are terrible for comapany morale. I've seen it many times, and heard many more stories. On top of the issue in this story, there are others too. For example, if someone wants to leave, but the bonus or vesting is coming up, they will stay, and you don't want people on a project who don't want to be there. As another example I know people who work at companies that are going…
If everyone is aware how the bonuses work and feels their 'fair' share is obtained, then it just becomes another part of the calculus.
I speculate as a non-manager that bonuses are a good way (in the federal contracting realm, from the company perspective) to incentivize employees without inflating their base salary to the point that the company isn't competitive for new work.