Compression can (in a way) be enabled for the whole repository by specifying compression to be enabled globally like so:
kopia policy set --compression=zstd --global
By default all snapshots inhert from global policy, and therefore, compression will be enabled for all backup items. You can of course override it for specific backup items.
As for the deduplication and compression, a recent change to the repository format introduced as part of V0.9 means that data compression happens after hashing, so it should in theory mean that deduplication shouldn’t be affected by compression at all. So it shouldn’t care whether or not compression was enabled, or what algorithm was used.