ok this is going to sound rather strange but here goes:
In the bible (and especially Revelations) if any multiple of 10 years (in this case 1000) is use it is not talking about the literal time, it is instead referring to a complete set of time, this set could be any number of years and would usually require some outside knowledge to know the actual time.
So lets apply this
1000 years since NM sealed: complete time set of Celestia ruling alone
1000 years since Discord sealed: complete set of time when harmony ruled
1000 years for Crystal Empire: complete set of time that Crystal Empire was gone/Sombra was gone