The gemarah Megillah 16b indicates that the Mishkan in Shiloh was destroyed. There does not seem to be any outright statement in the pesukim that this is the case. It says (Shmuel Alef chapter 4) that the aron was taken captive, but does not explicitly state that the entire Mishkan was destroyed, which I would take to mean the full structure was completely decimated in a manner similar to the way the temples were destroyed.
From where do we know that the Mishkan in Shiloh was in fact completely destroyed?
For reference see the sources in this article including: Yirmiyahu 7:12-15, and 26:6,9, Zevachim 118b, Rambam on Mishnayos Zevachim 14:7. CF the Hebrew wiki entry