Using only Acetonitrile and Water and no additives is fully compatible with the Column and will not damage it.
We might however recommend having 0.1% Formic Acid during Column Storage to help inhibit bacterial growth. You should change your Aqueous Solvent more frequently in this case for the same reason.
If you find the Peak Shape is not as good without Formic Acid, try using a steeper Gradient to sharpen it. Some compounds’ retention and/or peak shape may be significantly affected by the presence of a Mobile Phase additive and others may not. It depends on various factors pertaining to the analyte, the Stationary Phase, and so on.