It seems like the DLCs of credit & customes won't appear neither inside the game folder nor in the game if you download the game from GOG galaxy directly.

I had the older version of the installer stored in my disk, and tried to reinstall the game with it. Those dlcs indeed exist in the old version (17654), and they're actived by default. Then I updated the game to the new version by using GOG Galaxy as well as the entire dlcs. Fortunately the missing DLCs remained in the game folder. When started a new game, only contexts in the notifications of those three dlcs (credit & customes) are missing, while the others are normal.

So I guess those dlcs are indeed excluded in the newer version. I don't know if other people also have this problem. But I'd appreciate it if you gog or devs could check it.

Thanks.

Yes, everybody has this "issue". The three DLCs that are now removed were never listed in the DLC package and they were removed in the actual update which was probably intended otherwise the description would still be there when you use them. However GOG also included three addiitional DLCs preinstalled with the base game which probably was not intended since those are also part of the new DLC package 2. See more about it here:

https://www.gog.com/forum/general/release_megadimension_neptunia_viir_arrives_with_a_60_discount_1ca60/post61

I would suggest doing the following:
1) Install the game using the actual installer (and therefore get the three new DLCs).
2) Use the old DLC package installer and then archive the DLC folders 1,4 and 5. Uninstall the old DLC package installer.
3) Install the actual DLC package (because some of those DLCs were updated) and if you like simply copy the missing and archived folders back into the DLC subfolder. You can enable/disable the DLC 1,4 and 5 by editing the neptunia.ini in your savegame folder.

Regarding HDN2 and HDN3 let me quote something from the link I posted earlier:

"It's worth noting that if you go by the DLC folder numbers, Neptunia Re;Birth 2 also has a missing DLC (9) while Re;Birth 3 has several (4,10,11,12,13) "

So yes, it seems as if there's something missing as well. I still have my old installers archived and will check this out myself at a later time. However I guess that the solution to keep these missing DLCs is as simple as it was with HDN1.

Edit: Just tested HDN2
The old base game has no DLCs preinstalled and with the DLC package installed you get the DLCs (folder names) 1,2,3,4,5,6,7,8,10 and 11.
The actual base game has the DLC 1,2,8,10 and 11 preinstalled and the DLC package adds 3,4,5,6 and 7.
This means the DLC #9 is missing in the old and the new GOG version so there's no need to keep the old installers since you won't miss out a thing using the actual installers.

Edit2: Last but not least HDN3
Old versioan and actual version installs without any DLC and the DLC package that are installed are the same (old and new version is missing out a bunch of numeric folders) - so you should also take the actual installers here.

Summary: The problem only exist in HDN1.

Thanks for your help! Luckily I have the old installer of HDN1 downloaded before. Maybe I'd better to download the installers of 2&3 now. Lol.