Possible reasons: part count, reliability, lack of concerned about that that level of leakage, avoiding complexity.
To expand on leakage current being of little concern: 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 47,600 hours of "standby" time (discounting battery self-discharge). 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.
Thus, the expected use of this board is not greatly concerned about leakage currents in comparison to the 100 to 1000+ mA loads the battery will see in normal operation (e.g. phone charging, running an rPi).
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.
Note: the proposed 200k pull-up and 400k pull-down with switch circuit would not work. From the datasheet, The device is put into operation when EN is set high. It is put into a shutdown mode when EN is set to GND. This looks to be a normal logic input, so it is intended to be driven close to the rails. It is not a comparator input like the LBO pin or certain other regulators that have precision-threshold enable inputs.