Do you need to take the shelf out to spot clean? I'd just do visible bits. At least for a while. If no visible bits then leave it
I know with our robo I don't spot clean because there's nothing to find to spot clean - I change his sand in his sand bath maybe every two weeks (it gets lots of poops in). And wait to do a partial cage clean. One thing I really found helps which also might work well for a dwarf hamster as well as a robo. Is when you come to do a partial cage clean of the substrate - just do one half - the left half or the right half. So they can still feel safe and familiar in the other half. Then maybe in 2 or 3 weeks do the other half. Still just spot cleaning really but it's an opportunity to take out a house eg and check under it.
Our Robo actually had two nests - one at each side of the cage - so if I did one side of the cage he'd move to his other nest and then vice versa. Less upheaval for them.
You shouldn't really need to take a shelf out to spot clean - it is very minimal.
And yes best not to disturb any cage contents for at least two weeks - they are still easily freaked during that first two weeks.