I like my navigation keys on the main layer, although on a board with thumb keys for modifiers and layers, I'm okay with them being on a 2nd layer.
I have 2 boards with layers, one is a DIY custom with thumb keys (48 keys total), the other is a 60% (KBT Pure, just got it). On the Pure, the default behaviour is to have arrows on "OKL;", but I find that rather clunky (due to the positioning of the Fn switch in relation to the arrows and trying to do shift+arrows for selecting text), so I switch the right mods into a permanent arrow cluster on the main layer.
On my DIY board, I have dedicated navigation keys, but I wouldn't mind having them on a layer, using home key positions (ESDF anf IJKL for arrows and PgUp, PgDn, Home, End). However it makes it difficult to design the layers, since I don't want too many layers and still need to fit in F-keys, numbers, symbols, etc.
Also, being able to do combinations like Shift+navigation, Shift+Insert or Ctrl+Alt+Shift+F-keys makes designing the layers even harder, but it's doable if you're careful with key placement.