Oh yes I remember about Mr Crumble. It must be very hard after something like that happened and I can quite understand some of your worries. Really though hamsters tend to be healthy and fine with very basic care and Syrians are quite a healthy species - you were just really unlucky with Mr Crumble. You are doing everything fine so please don't worry about every detail. I am sure it was nothing you did or didn't do that caused Mr Crumbles sad early death.
If this helps with reassurance, then when we first had Charlie he nested in a little round plastic house and when I cleaned it out his hoard had turned to mouldy compost under his nest (it was enclosed and the plastic sweated and he'd hoarded lots of broccoli and wee'd on it. He was fit as a fiddle. I've had bits of substrate grow fungus on them after a water bottle leaked and he had a cage full of breeding moths not long ago (nightmare). They can survive many things and be perfectly healthy, just as humans do, as they have common sense and an immune system. They have good little instincts and eat what they need.
I know it isn't easy to be reassured because basically what happened to Mr Crumble was a trauma. And hopefully in time, you will be able to be less anxious about your new hammy. We all get anxious about them to some degree, like Mother hens, but there is only so much we can do and nature has a mind of its own.
How much do hamsters eat? Very little. They hoard most of their food. I find they like eating in bad and snacking from their hoards, rather than eating out in the open, which is partly why they like hoarding under their nests. They also drink very little as well. I used to worry that I couldn't see the water bottle go down much - I still can't. Sometimes they only drink at night as they sleep during the day. Charlie used to get up for a drink mid evening sometimes, but not always. So you might hardly ever see him eat and drink, but they will take what they need. With regard to the peanuts - that peanut will be a prized treasure to save for an extra special snack (maybe only on Sundays!) Half the pleasure is cracking open the nut to find the peanut and then put it in a special place. Charlie put a peanut in his potty recently just to make sure no-one took it (worst place possible to put it Charlie).
You are quite right though, there comes a time to have to clean out the bulk of the hoard. And I guess pruning it during a cage clean is a good idea. If most of the food is fine and dry though when you change the substrate, then replacing most of it is fine too.
What you might find reassuring is what people recommend - weekly health checks - there's a thread on here somewhere showing how to do a weekly health check, including weighing them. Have to go now I'll add a bit later
Don't worry about mites