Are duplicate variants against the VCF standard?
No. The only point the specification makes is that:


  It is permitted to have multiple records with the same POS


I suspect this is intended to let the file list different variants occurring at the same position, but this incidentally allows duplicate variants.

This said, you probably don't want duplicate variants, because it will mess with any statistics you apply over the variants, and will unnecessarily clutter the file and slow down processing, if this happens a lot. You might also get variant annotations on one variant but not another, which can become a problem depending on how you query your variants.