There are is a minus to the approach Apple have taken with Launchpad: users such as yourself who like to organise their apps into subfolders have to either avoid using Launchpad or perform this organisation in two places.

However I think the way they have implemented it provides for more flexibility, especially in multi-user systems. On my account’s Launchpad I can arrange and group the app icons any way I like, even delete them, and know that all the apps I have will still be found listed under the root Applications folder. Other users of the system can also do the same without impacting how my Launchpad looks.

Aside from this flexibly I have found it was still best to avoid moving apps into sub folders for two reasons. The firstly is that while apps generally did behave themselves after a move, and it was only the occasional one that was poorly coded and didn’t function properly in a sub folder, it was still a change that impacted all users of the system and it could be confusing to impose my own app movement and groupings on other users. The second reason is that nowadays many of my apps come from the Mac App Store. I find the App Stor’s installation process makes the app’s folder read-only, with app updates performed from the App Store updates tab. I’d prefer not to move them and break this model.