Hashem has a hidden abode where He cries over the glory of Israel that was taken away… [after the destruction of the Holy Temple and subsequent exile], and over the desecration of the glory of the kingdom of Hashem. (Chagigah 5b)
Rav Tzadok explains that after the destruction of the Temple, Hashem changed the way He interacts with the Jewish People. Prior to the destruction, Divine providence was easily discernible. After the destruction, Hashem concealed His guiding presence and it looked as if He had abandoned the world and His people. In reality, this was not the case. The holy presence of the Sh’khina remained connected to us through all of our sufferings. However, Hashem’s watchful providence was no longer discernible.
While Hashem’s presence is concealed, we may be subjected to suffering until the rectifications are completed, leading us to do t’shuva (repentance). Hashem’s crying in His “hidden abode” is the concealment of His presence. When we suffer, Hashem cries with us.
Based on Rav Tzadok HaKohen on the Parsha, By Rabbi Yitzchak Schwartz, Devarim