The changes to mission difficulty were entirely limited to the first three towns in the game, which means missions from levels 1-15. We didn't do anything to missions above level 15. So no, they shouldn't be any harder now than they were in late closed beta or open beta. Of course, tuning on ships and skills, etc. is ongoing and it may be that the stuff you were playing with at that time has changed since then, but there was definitely not any kind of a mission difficulty pass above level 15.