It's not really considered "bad" to put folders there, but (as you've seen) it can cause problems with some apps.
The reason the updates are failing: The installer/updater looks for an app in the /Applications folder and doesn't find it. So, it assumes the app is not yet installed and that you are trying to install the whole app from the update, so it fails.
Alternatively, the app could be duplicated because the updater doesn't find the app and decides to install a new copy.
To avoid this problem, here's what I recommend:
Create another "organized apps" folder somewhere.
Make folders in it as you have in your /Applications folder.
Open one Finder window to /Applications and one to your new one.
Select ten apps from your Applications folder. Right-click and choose Make Alias. Give it a second. Then, drag the aliases you've made into the new folder. Repeat this (ten apps at a time) with the rest of your /Applications folder.
Now, you've got 'links' to all your apps in your new folder. Organize them how you want. You can now double-click the aliases in that folder to launch the apps they correspond to. Feel free to re-name and reorganize these aliases as you want.
Note that, with this method, updates should work. You will, however, have to manually add each app you install to the other folder.
That’s not the recommended way of configuring a two-disk OS X install. Steps:
- Make a clean install on the SSD. Or you can just copy over the System Files. This would make steps 2 and 3 unnecessary.
- Create a temporary admin account on the SSD.
- Add a new account in the Users and Accounts preferences. It should match the credentials of your old account on the HDD.
- Right click on the account after it has been created, then click on Advanced Options.
- Set the home folder of this account as the previous home folder on your HDD.
- Transfer the necessary apps, libraries, etc by using a disk cloning app or good old copy-pasting.
The Download folder reappears because OS X thinks that the home directory is on the SSD, not on the HDD.
Source: http://macintoshhowto.com/hardware/how-to-speed-up-your-mac-with-a-ssd-drive.html
Best Answer
The two hierarchies are separate, and cannot be kept in sync without third-party intervention. Even then, there would be difficulties. Note that Launchpad folders have capacity limits that actual folders do not have, and folders within /Applications can contain nested folders, while Launchpad folders cannot.
It's just a coincidence that the apps in /Applications/Utilities match up with the Utilities folder in Launchpad. On my machine, I moved Terminal out of the Utilities folder in Launchpad, but it's still /Applications/Utilities/Terminal.app