Yes, they are a bit mysterious. The winged dragons of post-Angband Middle-Earth -- such as Smaug -- must have been released, or perhaps were the descendants of those that were released (Thorin says that they 'bred' in the Withered Heath), in the last assault upon Thangorodrim. It is recorded that that is when Morgoth finally finished their design.
Presumably, some got away in the battle when they realised they were losing, and hid as did the Balrogs in the mountains of the North.
The 'cold-drakes' of the Grey Mountains are even more myaterious. There is firstly the fact that we don't know what a cold-drake was; was it a dragon that breathed freezing air instead of burning? In Tolkien's earlier writings, there were three sorts of dragons, some being 'cold like snakes or lizards...'. So maybe the later cold dragons were simply these gigantic, cold-blooded lizards, or maybe they really were 'cold' as opposed to 'hot'.
These may have got out into the Grey Mountains before Angband was overthrown, if they didn't fly. If they did, then they too would have escaped from the War of Wrath with the ilk of Smaug.
Why were they put up with? I don't think you can suppose that they could have been dealt with. Dragons were certainly far too hard to kill.
It would be an interesting question, though, to ask why Sauron and the drakes of the North never teamed up. They logically should have. Gandalf mentions the prospect of Smaug being used by Sauron, which was dangerous, but what about all the others? He may have been the mightiest and the closest, but there should have been others -- in particular the aforementioned cold-drakes.
Did they simply kill each other? Had they all fallen asleep?
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