By default, K3S will run with flannel as the CNI and use custom directories to store CNI plugin binaries and config files(You can inspect the kubelet args K3S uses via journalctl -u k3s|grep cni-conf-dir).
So you need to configure that properly When deploying Multus CNI.
For example given the official Multus manifests in https://github.com/intel/multus-cni/blob/36f2fd64e0965e639a0f1d17ab754f0130951aba/images/multus-daemonset.yml, the following changes are needed:
volumes:
- name: cni