Yes Sheer Force will boost all moves that have secondary effect(s), but it actually depends which Pokemon the secondary effect applies to.
Sheer Force only applies to moves with secondary effects that affect Pokemon other than the one using the move.
Dynamic Punch is therefore not affected by Sheer Force, as it affects your own Pokemon whether it flinches or not. It's the same with moves that inflict recoil on the Pokemon using it, e.g. Brave Bird, which Sheer Force will not boost, but if the move has another effect, e.g. Flare Blitz's burn chance, Sheer Force will boost.