As mentioned, the designs of the two cars bear little similarity. On the e85 the motor sat under the roof itself, where rain water could drain by it, when the drains were blocked, these areas filled with water and the motor eventually corroded and stopped working.
On the e89, the side vents are to allow for air to pass through the boot in order to remove any battery fumes and so forth. These were found to allow water in under some circumstances, though I've not heard of it being sufficient to penetrate the battery area (not to say it couldn't). These vents were a recall, the roof motors on the e85 was not.
In any event, should the motor ever fail on the e89, it can be accessed easily for replacement in the boot floor. On the e85 it required the entire canvas roof to be removed. IMHO, its not a concern for the e89, I'm sure there are other weak areas that will show over time, each car has its own common faults.