Jaggy, some thoughts from a flight test specialist:
the winglets are nearer vertical than horizontal, so their contribution to lateral stability will be tiny. They will shift the lateral position of the centre of pressure outboard slightly, but the shift will be very small - think how much wing area is inboard compard to outboard, and also remember the CL distribution along the wing span favours the inboard part of the wing also, so changes to the tips do very little to the lift distribution as a whole.
Longitudinal CG change will be negligible compared to other factors such as fuel, cargo and passenger distribution in the aircraft.
The winglets main function is to extract some energy fom the tip vortex that would otherwise be lost, and convert it to a small forward thrust force. They also slightly increase the wing efficiency factor, thus reducing induced drag and increasing the L/D ratio. This gives increased range and less fuel burn for a given sector, which saves operators a lot of money, as I am sure you know! This also will affect climb and descent peformance, and potentially takeoff and landing performance, hence the need for a different performance database in the FMS for some aircraft types when winglets are fitted.
As for changes to cross-wind limits, it may be that the flight manual limits are simply that which has been demonstrated by the test team, thus they can gaurantee the aircraft's handling characteristics will remain safe and within certification limits.
Aerodynamically it is hard to see why crosswind limits should be different with/without winglets, unless they are affecting directional stability, which could be possible given their size and orientation. If they make the aircraft slightly more directionally stable, then it would be harder to kick off the drift for a crosswind landing, hence the slight reduction in the crosswind limit.
Hope this helps.