You could call it that. The term "timberclad" is not an 1860s one, but rather a back-formation, based on the terms "ironclad," "cotton-clad," and "tinclad," which were in use then. In general, a gunboat not protected by much more than her own structure and maybe some added timber was usually just called a gunboat. (Incidentally, not all of the "tinclads" were in fact protected by metal armor; it was just something of a derogatory nickname referring to their low level of protection compared to the ironclads.)