depending on how you capture that energy there will be waste of some kind that is created either in the manufacturing/growing process for the capture system or as a byproduct of converting solar energy to another form that is more easily stored. one of the advantages of diverse biological systems is that you can have cycles of organisms that process waste back into energy sources using solar energy + reactants as input. a self-sustaining silicon-based life-system would probably end up following a similar pattern to process waste back into useful resources, because waste products probably cannot be avoided.
You're absolutely right. Silicon based 'life' system does have the advantage that it would not be restricted to Earth environment - it can probably also adjust itself in way that biological beings here on Earth cannot easily achieve (genetic engineering are almost always generational, software engineering is the complete opposite).
