Can? Yes. Should? Maybe. If the chocolate is melted and evenly dispersed through the dough, you could compensate for the decrease in sweetness by increasing the sugar (bittersweet chocolate is 35% to 50% sugar, so add between a third again as much and half again as much sugar as the amount of chocolate called for in the recipe).
If the chocolate is in chunks, however, you will probably be put off by the taste of biting into a lump of unsweetened chocolate, no matter how sweet the cookie surrounding it is.