They can, yes. IL2 is a bit strange since it stops sending telemetry when the window focus changes, so if you change a setting you wont feel the effects until the game window regains focus.
All of the IL2 effects under the 'shake master' are duplicates of existing effects in IL2 natively (that I personally thought are done poorly so implemented my own in TelemFFB). You don't strictly need to disable the shake force in IL2, but it might be...weird... if you have both enabled at the same time