To L and the investigationinvestigators, Naomi Misora is only missing
Light writes down Naomi's name, resulting in her death by suicide. Her body is never found due to the specifications made by Light in the Death Note.
Source: Naomi Misora - Plot (Last Paragraph)
Given that Light specified that she would commit suicide and when L sees Naomi's photo they still don't know that Kira can kill besides a heart attack, there's no way to connect Naomi's disappearance to Kira.
If L was to take a leap of faith, and pull out the CCTV footage showing Light with Naomi, what can they do then? Light had a legitimate reason for being at Police Headquarters (in fact it was by pure chance that Light ran into her there, it wasn't planned like with Raye) and if they questioned him, Light could just as easily said he noticed that she seemed depressed and tried to help her which would backup the suicide if they discovered her body.