essentially. Kunuka can be ambiguous (you can say nuka vibaya/vizuri), but kunukia is to smell good

adding the "ia" to the end is an applicative transformation which i think takes a minor part of the original usage and makes it the major part. so because "kunuka" is mostly used as "to stink" but also can be used as "to smell good", it takes the minor part of it "to smell good" and makes it the main meaning of "kunukia". https://en.wiktionary.org/wiki/Appendix:Swahili_verbal_derivation#Applicative

then on top of that it gets ma class plural inflected "ya" to match with "flowers", https://en.wiktionary.org/wiki/yananukia#Swahili