Kraken is v5. There used to be a v3 but that has been removed. v5 is deprecated and will be removed at some point in the future.
Helix, the new API, doesn’t use the same version numbers because it’s a separate system with different scopes, rate limits, pagination, and endpoints.
When designing a new app you should always use Helix where you can, only if an endpoint doesn’t yet exist in Helix should you use a v5 endpoint.