Let us remember that Poe based this fictional account of the Red Death--a disease that never existed--on the Black Death, a plague that notoriously swept through fourteenth-century Europe and decimating the population of vast swathes of the known world at this stage. The verse you have cited from the book of 2 Peter talks about the end of the world:
But the day of the Lord will come like a thief. The heavens will disappear with a roar; the elements will be destroyed by fire, and the earth and everything in it will be laid bare.
We can only imagine that, looking at verses like this from the Bible, that the original medieval people must have believed that the Black Death heralded the coming of the day of the Lord and the accompanying destruction that such an event involved. If we have a look at the ending of this tale by Poe, it appears there are obvious links to this verse that you have cited:
And now was acknowledged the presence of the Red Death. He had come like a thief in the night... And Darkness and Decay and the Red Death held illimitable dominion over all.
Both quotes contain the reference to disaster arriving like a "thief," in a way that surprises us all, and also contain reference to destruction and decay of all things. Thus it seems that Poe is deliberately alluding to such verses in the Bible that point towards the way in which plagues such as the Black Death were so radical and momentous events in history.