[Motion controls disable docked to undocked]

Just quickly detach and re-attach your right joycon when in handheld. Fixes the motion bug for me. 

[motion controls stop working when going from docked to undocked]

If you have no motion aiming in handheld mode after playing docked, just detach and re-attach your Joycon while in handheld. The game just needs the "please connect a controler" message to get motion aiming work again.

Edit: you have to disconnect your Pro Controller first when you switch from Docked to Handheld. Otherwise even the reattaching Joycon fix won't work. 
So it's: 
You play in Docked Mode with your Pro Controller -> You take the Switch out of the dock -> You go to the home menu and disconnect your Pro Controller in the quick menu -> You go back to Warframe and quickly detach and reattach your right Joycon. 
The game will then ask you to connect a controller. You have motion aiming now again. 
 

Weird fix but okay.