I never wake up my snakes, reach into their enclosures to handle them, or take them out of their hides unless it's an emergency. Doing so is called 'flooding' (a term used in behavioral science) and it doesn't build a trusting relationship with them.
You're right, and you made an excellent observation that some of your current practices are stressful for your snake - staying in the hide all of the time indicates this. I use a behavioral technique called choice based handling that has been used with multiple species including reptiles - it allows you and your snake to gradually develop a trusting relationship in a fear-free manner. Royal/ball pythons may tolerate being disturbed or picked up because these snakes tend to be on the shy end of the temperament spectrum, we are bigger than they are, and when we handle them just because we decide it's time to do so they can't do much about it.
But their hide should be their safe space. I might lift the edge of a hide very quickly to take a peek and do a fast wellness check but I'd never lift a hide and then pick the snake up unless, as mentioned, it's an emergency where they need to be evacuated.
I've used choice-based handling with all of my snakes, including some very shy and defensive individuals, and have consistently had excellent results. Using this has helped to calm my snakes and they will typically let me know when they are interested in interacting or coming out to explore rather than just staying in their hides.
As a side note - it sounds like you take your snake out of their enclosure to feed them? There's no need to do that - it's an old-school technique based on misunderstanding of snakes' feeding response. Just feed them in their own enclosure.
If you're interested in choice-based handling I will be glad to share resources with you.
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