Usually I don't watermark in 95% of the time, but today I had to for 50 photos. And its a bit of a hastle. If I do it in PS with acton it doesn't look good in vertical photos
Manually watermarking is the best I think, or just separate the vertical and horizontal photos, then create separate actions for them would be another option. Or use another third party software like uMark or Mytoolsoft Watermark
One more option is to Use LR to Open Files in PS. Finally, you can select Files and then export with Watermark on LR. This works for me....