Yes, these will be used as regular Ashigaru. However, some of my Wako will be pretty well armored, as some actually were - here's Spanish governor Gonzalo Ronquillos account on the matter:
"The Japanese are the most belligerent people here. They bring artillery and many arquebusiers and pikemen. They wear body armor. All provided from the works of the Portuguese, whom they have shown to them for the detriment of their souls [sic] ..."