I honestly can't tell if she's kidnapped or hiding in her place. If she was kidnapped why would she let her keep her phone or question why she didn't call him?
The thing is that Yuri has no reason to hide Nagi. The kidnapping is more likely since Nagi had just cut ties with Reiji and if Yuri had known, she would have let Nagi return to Tokyo. Yuri probably met Nagi (or saw her with Reiji) and asked her why she was in the city; Nagi didn't respond; Yuri gets emotional and somehow Nagi ends up in the storage room.
Regarding the cellphone, it seems to me that it was in the house but not in Nagi's possession. Between us, it's very convenient for the plot that Yuri didn't get rid of Nagi's cellphone... And there's also the fact that the battery didn't run out after a week...
Why didn't Nagi call for Reiji? I think she may either be scared of what Yuri could have done or she doesn't think she deserves Reiji's help after cutting ties with him.