Is there any good midi controller with no integration issues with cubase?

Not exactly true. Whenever cubase starts, it copies the factory scripts to the public directory. The only way to avoid this except from disabling the factory scripts is to delete them from their initial location described here :

Backup and Edit the copy here to prevent that from happening:

C:\Program Files\Steinberg\Cubase 13\midiremote_factory_scripts\Public\novation\launchkey_mk3_49