Quite true, if you don't have permission to see the files in a user directory then these utilities won't size them.Not used WhatSize, but it looks similar to OmniDiskSweeper, which I do use. I also use Disk Inventory X, which is very pretty!
However, I don't think any of these utilities will pick up any files which aren't in the account you're running them from (which does make sense from a security point of view). I was struggling for space on my old iBook for months until I eventually realised that my Girlfriend had loaded 5Gb of MP3s onto her account. Neither ODS or DIX spotted that!