I like your water change system, and the bare bottom really make for a good plan on a pico tank. People often struggle with water quality in these pico tanks and you have it nailed down. That "kaleiascope" brain is WICKED. They are my favourite type of open brain.
As far as shocking the system goes, it appears as if you are probably
not shocking the system. Consistency is always important, and if the tank is
used to getting 100% waterchanges then that is consistent for that tank's inhabitants. I'm a firm believer that different systems react differently because of different maintenance. People can essentially achieve the very same thing (a thriving reef) by performing a myriad of different maintenance schedules. Even taking a peek through TOTM threads on ReefCentral or here on CanReen you will see
very different maintenance habits.
However, if you're ever concerned, or you just want to experiment, you could always perform your waterchanges the same except add back 25-50% of the "old" saltwater. You would still get a thorough clean. I would suggest you put the water to reuse in a bucket on its own rather than allowing the corals to sit in it though. I'm not sure that is clear... so you would have say 50% of the water in one clean bucket and 50% of the water in the bucket holding the corals, then clean tank, add corals to tank, add water to tank from the clean bucket, and toss the water from the bucket that held the corals.
You're definitely making me take a second look at the 5-gallon Fluval tank I have sitting in a closet...