Baby Syrian hamsters are babies basically and easily scared
So the main thing is to give it a bit of time and patience so he learns to trust you. Start by talking to him through his cage so he gets used to your sound and presence and familiarity, and offering him the odd treat through the bars when you see him. As you've had him three weeks, you could try some out of cage bathtub bonding maybe twice a week, if he seems interested in coming out - eg if he comes to the door. Or if you see him you could offer him a "taxi" (A large rat tube makes a good taxi) for him to walk into. Then make sure you have your hands over both ends when you life him out and take him to a hamstersafe area (eg bathtub or playpen) where you can do the next stage of familiarisation (I've linked our taming guide below).
Baby syrians do tend to pee in their nest until they've developed better habits, so you will need to spot clean that out, which will upset him but it's partly what stops them doing it once they realise their nest has been disturbed.
So you'll need to scoop out the odd handful of pee'd on bedding and food in the same area, but try and keep it minimal and leave everything else undisturbed. And if there is the odd bit of hoard that isn't wet, leave a little bit of that in for now as they can get quite frantic if their hoard is "stolen"
Likewise if you can leave a little bit of smelly nest bedding (that isn't wet but might be whiffy) it helps. And also put a handful of new food in next to the nest (trains him to keep his hoard slightly separate). They don't stress as much if you replace some of the hoard after removing it.
Then tear up some sheets of soft plain white toilet paper and tear each sheet into strips until you have a pile of strips, and put those in his cage near where he was sleeping - not actually in his nest but outside his house (or similar) and the hamster will pouch those and take them to rebuild the nest with.
He may keep doing this for a while though, while he's young, so you may have to repeat the process a few days later, but I wouldn't do it every day or it'll really stress him out.
The poops you don't need to worry about really. They are like little hard black seeds and not really dirty or smelly. Hamsters can actually eat their poops (normal) as they have two stomachs and can redigest nutrients from the poops - likely to be hard wiring for living with food shortages. Which is why they are hard wired to hoard as well.
So generally with poops - don't worry about them - if they start taking over a bit in the cage you can spot clean them out but it's not essential to remove all of them. Particularly in the nest area as that is also robbing his food store! But if they are also wet then they'll get spot cleaned out with the pee and wet hoard.
Hamsters will use a litter tray and some will use a sand bath as a toilet. Does he have a sand bath? They often choose a corner of the cage as a toilet - unless it's very deep bedding and then they are lazy and pee under the bedding. They are actually quite clean little things and usually prefer to keep their pee separate from their nest and hoard - but they need to develop a bit to keep good habits
It's only their pee that is unhygienice - they wash/clean themselves regularly and groom daily.
Hand taming a hamster can make life with your hamster very rewarding. Suddenly they will sit on you to be stroked or even go to sleep on you, and will be very easy to handle. It can take a bit of time and patience initially.
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. One more question if I remove his hoarding and put fresh seed mix their like exchanging , will he understand this ? Does he recognise what he has collected and which is kept there not same