The merging will ensure, that the merged photo will appear in all albums, as Mark pointed out.
But there are some things you still have to manage manually, particularly, if the photos are shared or scanned photos, where you added metadata manually, captions, keywords, dates, locations. Then the two photos to emerged may have different metadata, and the Photos.app will just keep the metadata of the version it is keeping, because it will not know, which of the metadata are the best.
Also, the photos may have slight differences, and photos will have to decide, which is the best version. That is not always the version I would have liked to keep. when I let Photos merge two photos, I am adding them to an album before I merge them. This way it is easier to check, which photos I need to recover to get the version back, that I like most. Here is screenshot taken on my Mac before merging two photos with slight differences:


Most of the duplicates shown by Photos are duplicates I created intentionally, because I need two different versions if the same photo, for example two different Live effects - a loop and a long exposure effect, or the original and a cropped out section to show the details. I am only letting Photos merge the photos, if it says that the photos are identical.