Not recommended to do ATF flushing due to the following reason:

a) Most shops uses a machine to flush ATF fluid. The machine had gone through many cars and metal shavings could be caught inside the machine and transfer into your car's AT gearbox.

b) By flushing out all the old fluids, it might cause slippage on your old transmission.

I strong suggest you just remove the transmission oil pan, replace the AT filter then fill your car up with fresh fluids up till the acceptable level.

Yes you should. Myvi have an ATF filter inside gearbox. You can change it by removing the ATF pan.