There is simple answer to this question, as it depends on your experience and what you plan to do with the molecule. In most applications, the thiol will be reduced just prior to use to ensure that unwanted dimers are cleaved. If the conjugation is to a maleimide, the reduction can actually be done in situ during conjugation. In that case, there is very little difference. Technically, it is easier to purify a protected thiol, but it is very difficult to keep it on completely intact.