No. Similarly to how your licenses work for Confluence and JIRA, the Gliffy license must be purchased separately for each product.
As of July 1, 2013, all Gliffy Plugin license purchasing is done through the Atlassian Marketplace and your my.atlassian.com account. Unfortunately, Atlassian considers Confluence and JIRA to be completely separate products and you must purchase a license for each if you want to use Gliffy in both. There are no current offers available for discounts if you purchase both at this time unfortunately.
If you have further questions, please contact Gliffy at email@example.com or Atlassian at support.atlassian.com. Thanks!