The deprecated DHT API commands in the RPC client have been removed. Instead, use the Routing API.
The legacy subset of the Kubo RPC that was available via the Gateway port and was deprecated is now completely removed. You can read more in ipfs#10312.
If you have a legacy software that relies on this behavior, and want to expose parts of /api/v0 next to /ipfs, use reverse-proxy in front of Kubo to mount both Gateway and RPC on the same port. NOTE: exposing RPC to the internet comes with security risk: make sure to specify access control via API.Authorizations.
The Object API commands deprecated back in 2021 have been removed, except for object diff, object patch add-link and object patch rm-link, whose alternatives have not yet been built (see issues 4801 and 4782).