Moral dropping for no reason on certain planets.

have you been raising taxes or has population started geting up there past 20B? As you get higher population the dropoff of morale gets sharper. That could be contributing to the problem. I've found at 20B population you usually need about three Virtual reality centers to hold good moral and a decent tax rate. Above 20B the morale dropoff gets pretty extreme up to 25B. At that point there is no further dropoff, but you will have a planet half covered in VRCs to keep them happy.

Is it me, or does the actuall effect of bonuses wear off after a while?

There is another morale bonus, not well documented, that applies to planets of PQ 11+. I think that when smaller planets get to a certain population level, the lack of this bonus gets magnified by the increasing population.

Check your low-morale planets; what PQ are they?

Your moral's dropping? Maybe you're just evil.