The auto ISO behaviour with a hot shoe flash is quite different for each camera.
I have used hot shoe flash on D5100, D7000, D700 and D4.
I only shoot in M mode. Min shutter speed I use depends on the picture lens and aperture combo, typical 1/30, 1/60, 1/125 inside room or hall.
I like to use auto ISO & hot shoe flash with the D5100, D7000 & D4. Not the D700.
The D5100 and D4 auto ISO automatically switches to ISO 400 when a hot shoe flash is mounted and usually I adjust the ISO to 800, 1600 or 3200 depending on the exposure meter reading. The camera will then automatically adjust the ISO to have a zeroed reading on the exposure meter or sometimes 1/3 or 2/3 EV under when it hits the max ISO limit. I also adjust the flash compensation.
The D700 will automatically switch to ISO 200 when a hot shoe flash is mounted. With the D700, I have to manually set the ISO to have a zeroed meter reading or sometimes 1/3 or 2/3 EV under, I have to manually set the ISO for every shot to balance the back ground & the flash. The auto ISO operation of the D700 with hot shoe flash is not as flexible as the newer cameras as it doesn't adjust the ISO automatically with hot shoe flash.
I do this is because I like my shots exposure to have a balance of light from the flash on the subject and light from the room or hall back ground, although it may be a little dimmer.