The usual "Khach" sound over speed bumps is from Bushes. What happened to me was when I had them checked, the mechanic just moved or checked them and they came in their correct place and all sounds were gone, simple as that. Have you got your car serviced recently ?
Steering is EPS. There is a motor under the dashboard, just under the glove compartment. If it's faulty, you many need to replace it. Or there may just be something brushing against road. Opening Vitz Dashboard is no Joke so be carful, especially those hinges, they are weak.
Alignment is normal maintenance once or twice a year. Do not worry about it.
Bushes are costly. May be 800-1000rs a pair for local ones. But 8000Rs is a bit excessive. Get an idea from market.