Possible reasons: Part count? Reliability? Not being concerned about that leakage? Avoiding complexity?

To expand on the leakage current, check the specification of the TPS61030: 20uA (typ). Then 1uA (max) in shutdown. What will another 20uA of leakage through the pull-up do? Expanding on laptop2d's calculations: 21uA leakage from a 1000mAh battery gives 47.6 thousand hours of "standby" time. Over 5.5 years! The self-discharge of the attached secondary cell and the usage of the device are certainly of greater power-loss concern than shutdown leakage! Leaving shutdown then trades pull-up current for the converter's quiescent current.

If you were using this for something other than a USB power bank, you might be concerned about battery life. However, long-lifetime battery operated devices usually don't come equipped with 4A-switch boost converters.