You're probably OK as the wheel was (hopefully) properly rebuilt rather than assembled on a production line. I assume it was the same wheel, rather than just a swap-out, as the hub motor is an expensive part. It would be more surprising if they did change the type of spokes, as that would mean holding stock of an extra part. The thread depth is a small fraction of the spoke diameter so shouldn't weaken it too much.
There are a couple of e-bike specific issues here which can increase the failure rate:
- The loading on the rear wheel is much higher than on a normal bike, because of the hub motor, batteries (often near the back) and extra-heavy steel frame (common, not universal).
- The large hub motor means that the spokes are at more of an angle relative to the rim. Unless special provision is made for this -- which it often isn't -- this increases stresses on the spokes (but not at the end that failed for you). The spokes are also shorter than standard, and the hub motor can make assembly harder.
We have an e-bike and it broke 6 spokes in a day (after probably ~1000km): 1 in the morning, 1 on the way home, then 200m later another 4. After getting new spokes from the manufacturer, we had the wheel properly rebuilt, and it's completely true, with even tension, and no broken spokes since.
If it breaks more spokes, I'll use the first set to patch the wheel up and order good-quality custom cut new ones for the LBS to rebuild the wheel. If not for the warranty aspect I'd suggest you take the same approach.