I think if it was bothering him, he would let you know

His ears would be down or he may be chucking substrate out of his burrow entrance. He wouldn't like it if it was smelly and bothering him. So as the others sa - your nose can be a guide, but also Albert's behaviour. Unfortunately, at some point, you'll need to do a partial substrate change and then things will get messed up a bit but he'll just rebuild them. For a tunneling hamster, I would be tempted to only do a substrate change in one side of the cage at a time. This is what I do with our Robos. Then one side of the cage still has burrows in tact and they can feel comfortable even though the other side is changed. Then maybe a week or two later, change the substrate (or half of it) on the other side of the cage. This way they never feel like everything has been messed up in one go.
If he has tunnels and burrows then it's probably not possible to spot clean them without them collapsing. So then maybe just leave them until you do a "half" cage clean of the substrate. You don't need to worry about staining, it's only if there are damp areas - but they pee so little it has probably evaporated! And if there were damp areas, I think he would let you know!