Yes Indexes affect performance of joins. Assume this logic where
For (in 1 to 1000)
select salary from emp where emp_number:=B1
End loop

In this case the inner query will be accessed by emp_number index and query will be faster.
If in this case there is a index SKIP scan on emp table then that means emp_number is not the leading column on the index.
2. Usually it should not if the tables involved has correct stats gathered. If not then oracle makes mistake and in that case you can put ordered hint to force Oacle use your preferred order.