At my house there are two (well, three) Lego collections. Mine, and my kids'. The rules are stricter for mine: the Lego isn't meant to be thrown around, dropped pieces should be picked up, it isn't to be left on the floor, it doesn't get brought all over the house, and it gets put away every time.
The kids' collections they keep in plastic boxes and they can play with it how they want. Sometimes pieces get lost. I try to impress on them the importance of keeping the pieces together and putting things away where they go, but it isn't always possible. It might be a lesson they need to learn the hard way. My kids are extremely respectful of my Lego collection but not so much of their own. So it is possible to enact rules they can follow, but there are limits.
One issue that can help with missing parts is keeping track of where the parts should be. Keeping all the parts in one big box makes it harder to tell what's missing. If you keep your kits assembled as per the instructions, you'll know the parts are all there. Of course, this dampens your ability to create your own things, so maybe some other organizational method will help. You could sort the parts into ziplock bags by colour. You could put all the minifigs and their accessories in separate bags. Having enough smaller containers that lets you see when pieces are misplaced (i.e. not lost, but in the wrong container) helps you find pieces when you need them. Being able to estimate if a certain bag is missing pieces, or plainly recognizing that a certain piece is gone gives you the motivation to search for it now before the vacuum gets it. Keeping organized helps prevent problems. But it's also a buzzkill for many people.
That said: pieces will get lost. They will get broken. They will change colour in the sun. They'll lose their clutch power. So how do we cope?
The easiest solution is to order replacement parts from either Lego itself or from vendors on a site such as Bricklink. Some pieces are rare and hard to replace, but other pieces are easy to find and cost just pennies. Bricklink is intimidating at first but it's reasonably well structured and you can eventually find what you need.