how to choose the right pullup resistances for i2c lines with multiple slaves
You can't work like that.
You have no idea what is inside a chip and thus the moment you turn the power off you have no idea what the inputs will do. They can have a low impedance path to ground or between the two lines. 

A system like yours needs isolating switches which disconnect the device when it is powered off. Have a look at transmission gate chips. 

In general you design is violating good design rules. Using GPIO pins to power boards: horrible! Just use a power switch: 
https://e2e.ti.com/blogs_/b/powerhouse/archive/2016/02/03/when-to-use-load-switches-in-place-of-discrete-mosfets