If both watches were predominately used on land for 5 years, the answer to your question is no. Both will have the same likelihood of failure, regardless of rated depth.
If both watches were pressurized to their respective depths for 5 years straight, then returned to land, then the answer is yes. The seals in the deeper watch would exhibit more compression set, and would be more likely to fail under low pressure.
The depth rating is predominately determined by the case and crystal. A 100m watch and a 2000m watch will have basically the same seal design.