I think it's more likely to be a concentrated point of contact on the wheel. If the pressure is more localized than it is on the road (dunno if it is or not), then the rolling tension changes in the wheel would be exaggerated. If (poorly built) wheels have a tendency to go out of dish over time due to failure to adjust spokelines and stress relieve, then this process would be accelerated.
I guess if you ride crooked, this would be even more of a force concentration on the spokes of one side of the wheel.
This is the first I've heard of any trainer effects on wheels though...