The link-based approach is more robust and imposes fewer restrictions on the structure of the document. The $OnAdd approach uses simpler action code and is thus easier to understand and implement correctly.
To expand a bit, the link-based approach is more robust because changes to source notes are automatically propagated into data-point notes. For example, if you find an error in one of your source notes, you can just change the source note, and all its data-point notes will be updated automatically — no further action is needed on the part of the user. With the $OnAdd approach, after you correct the source note, you have to ensure that the $OnAdd action is rerun on every data-point note that uses that source, which in turn means you must remove all the data-point notes from the source container, and then add them to the container again (you could also use a stamp, but you must then ensure that your stamp and your $OnAdd action remain in sync).
This basically requires that with the $OnAdd approach, you keep all data-point notes as children of their source note, and if you want your notes organized in some other way you have to use aliases, which bring their own complications and limitations. By contrast the link-based approach allows you to structure your document and organize your notes as you please, since the connection between source and data-point is represented by a persistent link, rather than by the parent-child relationship.
The advantages of the link-based approach are largely independent of map view. Any large or even medium-sized research project would most likely have too many notes to yield a coherent map anyway. (I personally almost exclusively use outline view in documents that use this approach.) And there is no need to keep all the notes in one map — organize them in whatever way you like.
TL;DR: If you’re happy with always having data-point notes as children of source notes, or don’t expect to have to augment or change source data once it’s been entered into the data-point notes, the $OnAdd approach is simple and effective. If you want more freedom in your document structure and want to make sure that changes and augmentations to the source notes are always propagated to all the data-point notes correctly, the link-based approach is a better choice.