They do find it stressful, particularly when you haven't had them long and they're young. Some hamsters more so than others. Our last Syrian was particularly OCD and would get extremely stressed (and grumpy) if anything moved even half an inch!
Generally it's recommended to leave them alone for 2 or 3 days to settle in and not change anything or do any clean outs for the first two weeks. If it needs a bit of spot cleaning after a week then that should be ok if it's just say a handful of pee'd on substrate taken out and a new handful put in.
When they first settle into a cage, they scent mark everything - this creates a trail so they can find their way around (they don't see well). Hence they generally don't like things being moved. Adding new things seems to work ok as it's interesting and doesn't change anything existing.
Clean outs are stressful for them generally and my big tip would be to use a litter tray as Syrians will use it (if you put it in the right place - ie the place they have chosen!) and then the cage needs less cleaning - you just empty the litter tray every 5 days or so.
Although pet shops recommend cleanouts every week this isn't necessary and not good for hammies. You can go much longer than that with a litter tray and occasional spot cleaning, and the more substrate there is the longer you can go generally. Even then it's best to do "partial" cleans. eg if you change the substrate, replace some of the clean old substrate and mix it in, or sprinkle it on top so it still smells familiar. And don't do the wheel, toys, etc at the same time. You can do the wheel a different week and the toys a different week again.
Once they are settled in the cage, it is their territory and they don't like it being messed with! As they get older they tolerate a hand in spot cleaning better, although our Syrian still follows the hand anxiously to see what it is doing.
They are quite clean little things really. If they pee in the litter tray the rest of the cage stays clean and dry mostly. Don't worry about poops - they're not dirty or smelly - they are extra food supplies! They are like little hard black seeds and sometimes they eat them (for extra nutrients - they have two stomachs and can redigest vitamins etc from the poops) or hoard them for emergency supplies. So unless they start taking over in a big way I would leave them for now.
The other big thing they are stressy about is their nest and hoard. Even when doing a clean out, I leave those. Unless the nest or hoard is pee'd on and needs removing, but even then it's best to leave a bit of the old nest behind, and put a new pile of torn up strips of plain white toilet paper out so they can forage for it, pouch it and rebuild the nest, and replace any hoard removed with new food in exactly the same place. Try and leave a bit of the old dry hoard behind and add new food as well. If they think their hoard has been stolen they can start peeing on it to deter predators.
It also helps if they house that is open underneath and sat on top of the substrate - they like to bury their hoards under their nest and burrow down a bit. And it's more hygienic and less likely to need cleaning out. Our hamster once cleaned out his own house when he decided it needed doing! I found a pile of smelly substrate in front of the cage door and a hole in the substrate in the middle of the cage right down to the base, where he had taken it into his house.
Eventually when doing a clean, if the hoard has got really big and is taking over you can prune it a bit! But mostly it's dry food they hoard - anything wet of course needs removing or it'll go mouldy.
But if they are allowed to develop normal behaviours and aren't cleaned out too much they tend not to pee in nests and on hoards. A young hamster may sometimes pee in the nest as well as the litter tray, but they learn not to when the nest is removed!
You can use any kind of dish as a litter tray, but I like these open corner trays - they're a good size for a Syrian to sit in. They tend to pee in the very back corner (which is higher) and both ours then sit in the front part for a wash. So look out for where her chosen pee area is - it's often a corner of the cage. Put the litter tray there with Chinchilla bathing sand in (soaks up the pee) and a little bit of the pee'd on substrate on top, so she knows it's still her toilet area. And she should use it.
https://www.amazon.co.uk/Hamster-cor...=hamster+potty
This is the Chinchilla Bathing sand. I tend to get two at a time to save on postage, but one lasts me a few months.
https://www.viovet.co.uk/Supreme-Sci...q=sand&sct_r=1
With larger cages and plenty of depth of substrate you can easily go 2 to 3 months before needing to do a substrate change. It saves on substrate and can be even cheaper if you buy in bulk. Popular ones on here in bulk are Fitch (paper) and Hemp.
Have you got the cage sorted now so it works with things in the right places? If so give her 2 or 3 days to settle down again and hide the odd treat in the cage to distract her from the upheaval
She will enjoy finding them.
I've tried changing things when they're out of the cage so they don't see it and that doesn't help either! They then get anxious about leaving the cage and won't come out because they know what happened last time!