This comes from the old squabble that so much of science, especially biology, is reductionist in nature (everything can be reduced to physical and chemical mechanisms). Even some famous atheists have argued that not everything can be reduced (i.e. Ayn Rand who considered consciousness irreducible). So if something cannot be reduced (insert a leap of faith here) its complexity must be by design.
BTW the existence or non existence of God is not a scientific dispute since science deals with only concrete, observable and verifiable facts, not acts of faith. This discussion properly belongs in the field of Philosophy.
Not necessarily. There is the phenomenon of the "missing scaffolding" to account for. In other words, there may have been another part of the system that was required at one time, but has since gone by the boards. For example, building an arch would be impossible without supporting scaffolding; however, once the arch is complete the scaffolding can be removed without affecting the system.