If you are keeping him with good humidity, then most likely it's from before you got him and the way he was kept then. He's not bad. Keep up with soaks and humidity and good varied diet and it won't be very noticeable when he is larger.
The pyramiding is not that bad. If you keep the humidity up from this point on, you'll hardly notice the pyramiding when he's grown. What are your humidity levels?
He's is that way because you've raised him too dry. Is that walnut bedding in the bottom? Bad news. It's too dry and an impaction risk. I'd switch it out.
Spraying isn't going to provide near enough moisture to keep the humidity at an acceptable level. Buy an inexpensive hygrometer (humidity gauge) and check the humidity in there. I would bet it isnt much higher than the surrounding room (less than 30%). There are basically two ways to control the humidity in your baby's enclosure:
One way is to use a type of bedding capable of holding moisture, such as cypress. Keep the bedding moist and cover the enclosure to keep humid air from escaping. Obviously, don't cover it completely because he still needs some ventilation. The disadvantage is that most types of bedding that would work also come with a risk of impaction if your tort eats it.
The other option is to directly humidify the enclosure with a fogger / humidifier. This option can get expensive because you will probably need a humidistat to control the humidifier, and the complete rig will run you $100+.
One more thing. You really only need to worry about the humidity in his hut. It's easier to grt the humidity up in there than to humidify the whole enclosure. He spends most of his time in there anyway.
Well I switched out his bedding now to Eco Earth from here, I was just looking at old pictures and realized he had it when I got him. But I do soak him every day to every other day.
Oh, and he has a large water bowl that he can fit in and he sits in it all the time and he does have a hide.