What are these pull-ups for on BLDC driver reference schematic?
Looking in more detail at the app note it would seem that the pullups are superfluous. They are directly connected to the outputs of a GAL in the control logic diagram. The outputs of the GAL would be available within a few microseconds of power being applied.
Also the GAL outputs meet the voltage requirements of the L6234. As @MaybeJulius mentions there should be some interlock between the Vs and the 5V supply to ensure that Vs is available before voltage is applied to the control inputs. One of the options in the circuit is to make 5V available from the same supply in which case there shouldn't be a problem (but results in high dissipation in the 5V regulator).
If the control signals are being provided by a microprocessor it would also be safer to ensure that they are held low until the processor is running and has had a chance to initialize its output ports.
If the motor controller is not held in a benign state it could cause unwanted rotation or excessive dissipation in the motor coils by constant excitation.
A common way of doing that is to provide pull-ups or pull-downs to set the motor controller in an idle state. They will be overridden by the microcontroller I/O signals when it has configured itself.
In this case, however, I don't see why they are pull-ups and not pull-downs as the enable signals for the L6234 are active high. I would not consider it a good design as is.
L6234 datasheet