Is it possible to define (using only visual inspection of PCB and multimeter) whether or not SPI Flash memory can be properly programmed keeping the device In-circuit, without desoldering IC from the PCB? Or this can be found only via trial and error method? CPU specification is not available.
It may be possible. Based on the data sheet you posted, you need to see if Pin 9 is tied directly to ground, or can be controlled by the CPU. If it can be controlled, the chip can be re-programmed.
If Pin 9 is tied to the CPU, you may then be in the realm of trial-and-error to see how to control that pin.