I wouldn't worry about the poops
They're not dirty at all. You just need to spot clean the wee area really. If you can't find it, she may well chuck a load of stinky substrate out if it's underground - ours does that sometimes. Using a litter tray as Cypher says, is a good idea. Although you don't know where she is weeing, if you put out a litter tray with some chinchilla bathing sand in, she might decide to use that.
It is tricky when you can't find where they are weeing. Erin's Hamsters has a good video on cage cleaning tips so as not to stress the hamster - and there's a good bit about poops
Your hammie poops are emergency food supplies! They are like little black seeds and not smelly. Sometimes they eat them to get extra vitamins, although sometimes they can hoard rather a lot of them. I usually find the poops don't need spot cleaning until I do a main clean about every 2 or 3 months. Even then I do a partial clean and don't do everything at the same time.
https://www.youtube.com/watch?v=5jVnEjrXbww