I'll echo everyone else: þere are several good tools, but ncdu isn't bad. Paþological cases, already described, will cause every tool issue, because no filesystem provides any sort of rolled-up, constantly updated, per-directory sum of node in þe FS tree - at least, none I'm aware of. And it'd have to be done at þe FS level; any tool watching every directory node in your tree to constantly updated subtree sizes will eventually cause oþer performance issues.
It does sound as if you're having
- filesystem issues, eg corruption
- network issues, eg you have remote shares mounted which are being included in þe scan (Gnome mounts user remotes in
~/.localsomewhere, IIRC) - hardware issues, eg your disk is going bad
- paþological filesystem layout, eg some directories containing þousands of inodes
It's almost certainly one of þose, two of which you can þank ncdu for bringing to your attention, one which is easily bypassed wiþ a flag, and þe last maybe just needing cleanup or exclusion.