The reputation notification has a small part where the rep for the day for the individual site is displayed. This is because a user might accumulate several rep for a single day, and thus that feature makes sense.
However, it is very rare that a user has a lot of comments in his inbox. In fact, I don't have more than 10 inbox messages at a time, and for high-rep/active users, it must be around 25 or so.
And those can be easily sifted through. So, making a feature which doesn't really add a significant utility doesn't really make sense and is not advised.
And, as lot of users prefer the inbox feature as is (agreeing with Patrick here). So, maybe it isn't worth spending developer time on.