No, Candide and Cunegonde's relationship would not have been considered incestuous at the time. For one thing, sexual relations between cousins were considered perfectly acceptable in those days. Also, one should bear in mind that Cunegonde is an aristocrat, a baron's daughter no less, and for the upper classes marrying one's relations was not just permitted, but actively encouraged, as it ensured the continuance of the family line.

The aristocratic gene pool was, by its very nature, rather shallow, and so it was often virtually impossible to avoid marrying someone to whom you were related. In a later generation, Queen Victoria married Prince Albert, her first cousin, by whom she sired no fewer than nine children.

Voltaire, like the good philosophe he is, appears to be criticizing the unthinking subscription to tradition, a common refrain of Enlightenment thinkers. There's certainly no other explanation as to why Candide would want to marry someone as vacuous, boring, and shallow as Cunegonde.

In Voltaire's time marrying a cousin was not considered incest, for people did not realize the genetic risks of such unions.  In "Wuthering Heights," for instance, Catherine marries Sir Edgar, her first cousin and their is no implication of incest.

Do not forget, too, that Volaire is ever the satirist.  So, perhaps, he ridicules the custom of maintaining blood lines and the false pride taken in family heritage.