To reproduce:
1. Open Unity and download any asset from the store, close Unity
2. Find location of a downloaded package in PC storage (C:\Users\(user name)\AppData\Roaming\Unity\Asset Store-5.x)
3. In Asset Store folder create clean folder and copy there downloaded package
4. Open Unity, click create new project and click add asset package

Expected : Only one instance of package is shown
Actual : For every copy (made in step 3) of package there is instance of asset package

Reproduced with 5.5.0f3, 5.6.1p2, 2017.1.0b8, 2017.2.0a2

Won't fix:
The current package system is being replaced by a new package distribution manager hence this issue will sadly remain unfixed until the new system takes over. We apologize for the inconvenience and we sincerely appreciate your patience and support while we work to improve this feature.