Treatment of copper (0) with sodium hydroxide
$\ce{Cu(0)}$ will not be attacked by $\ce{NaOH}$, and will not decompose in this aqueous environment at room temperature. So, this is not to create some reaction with the copper. Two uses I can think of:


$\ce{NaOH}$ increases the solubility of $\ce{Cu2O}$, so maybe this is a way of getting rid of the last remaining copper oxide.
To bind the thiols with copper, you'd better be in alkaline conditions rather than acidic conditions, right? If so, then maybe this is the way of making sure you don't have any acidic groups or molecules remaining adsorbed on the copper surface, to improve bonding at the next step.