Both APIs have different implementations in the background but essentially work the same way from the developer side.
No matter if it's legacy or regular, the API key is used to access all Moralis functionality such as the Web3 Data API, Streams API, and Authentication API.
However, keep in mind that in the future, the legacy will eventually be removed and the regular one will be the replacement for it.
For future announcements on updates, please subscribe to Moralis Changelogs here.