Look at her at different times and from different angles, and check well their sleeping pouch, sometimes the joeys just change of position in the pouch and seem to have disappeared while they are in fact there, especially if there is only one joey (
the situation is a little different, but I've had the experience of one mysteriously appearing joey, after Oti went out of pouch, I could have sworn there was only him, and 2 weeks later his brother Teeboo mysteriously appeared in the nestbox, never knew where they hid him during that long because it did not seem that Frejya still had something in pouch).
There is also the possibility that they ate the joey for a reason or another... She will not necessarily show signs of distress if it happens when the joeys are not yet out of pouch (especially if she's a first time mother).