I had set Nautilus to show hidden files by default, yet wanted to deviate from it with my home directory. But each time I re-opened it with Nautilus, the hidden files were shown, so it seemed there was no per-folder memory when it came to this option.
I found an interview which mentioned Show hidden files is a per-window setting and has been stored per-folder since Nautilus 2.8 – but the key here is that it only does so in what is called the spatial mode. And Ubuntu, by default, comes with Nautilus set to the browser mode.
After catching up on this issue by reading The Spatial Way
by Colin Charles, I became a believer and decided to go with the spatial mode. The Gconf key which toggles between the two modes is /apps/nautilus/preferences/always_use_browser. After unsetting it, Nautilus now remembers I want to see my home folder without the hidden files by default. Yay!