Collect less junk! It’s ok to grab what you need, but many zomboid players are guilty of dragonhoarding. Do you really need that 25th hammer?
Build a burner shed/location away from your loot storage, preferably in a chunk of its own. Using this as a staging area, you can level tailoring, turn jewelry into scrap then bullion, or adding 5000 cabbages to your biogas units, all without adding data to your major storage chunks. Later, when this chunk gets chonk, we can remove it without it affecting parts of your base that you spent hours collecting and building for.
Design your builds like a functional house. The majority of the safehouses that are the biggest offenders of chonkies are builds that are just rooms of storage crates stacked on storage crates. Those spaces are not designed to live in, but to ONLY store.
Reduce your crate height to 1-2 crates max. This will force you to spread your loot over a larger footprint and that in turn will spread out the interactions across more chunks, slowing this process further.