After Several games (all different sovereigns) with B5+ i have never gotten the doom-day counter above ~25%, despite trying really hard (threat level 4-5, attacking SK outposts, expanding ..); and not doing anything overt to reduce it (e.g. lower doomsday spell). In B4 the counter was almost always 50-75% by mid-early late game.
Side note: my cities appear to attached more frequently than in B4 but by roving bands (bandits and the like), NOT by SK armies (suspect this is related to the doom-day counter issue). I am totally OK with this increase, makes proper city build up/defense planning more interesting.