the dynamics of low energy electrons in graphene is ruled by the Dirac eq. Strain will modify this equation adding a pseudomagnetic field (it looks like magnetic field, but it will not follow the same time reversal symmetry).
Free standing graphene will always have ripples, that what makes it stable, so in principla one should consider that in any calculations. The effect of such a ripples is well characterized. When graphene is on top of substrate, it will depend on the morphology of the substrate, whether strain is present or not.