In general, for a function to have an ##n##th derivative, it is necessary but not sufficient that the ##n##th partial derivatives exist.
Nobody can tell without knowing what identities you are talking about. The degree of smoothness required depends on the particular identity or theorem. You cannot make a statement like: "In vector calculus, all functions must be at least twice differentiable".
Of course, you can guess that if you have an identity with first order differential operators such as div and curl that are only applied once to each term, then typically the functions involved need to be once differentiable or continuously differentiable, etc. Sometimes, less is needed, if the identities are interpreted in a weak or distributional sense, for example.
When you are learning vector calculus with the intent to apply it, it is probably fine to (initially) assume that everything is ##C^{\infty}## (which is weaker than analytic). However, if you are interested in proofs, then you will see that this assumption is gross overkill.
Also, note that even innocently looking PDE with ##C^{\infty}## coefficients may admit solutions that become non-smooth in time. The development of such a singularity often has a physical significance, e.g. a shock in gas dynamics. Therefore, it is certainly not true that all phenomena of physical significance necessarily have smooth mathematical manifestations.