Lego will replace missing bits from new sets without argument. I’ve never had a piece missing, but had one damaged. No issue. Does take ages though, same if you order from Lego’s Bricks and Pieces service. I usually use Bricklink and I can create wanted lists from their digital designer program Stud.io.
I use these for sorting: https://www.bmstores.co.uk/products/multipurpose-tool-organiser-24-326366
I’ve probably got about a thousand or so loose pieces and I keep them sorted by type/size. The trays are really useful for this. Bricks in one organiser, sub-divided by size, plates in another, slopes & dishes in another etc. Easy to stash away when not needed.
For smaller pieces (tiles, technic etc), I’ve got three smaller Black & Decker organisers which are the perfect size.